diff --git a/.github/workflows/fetch_all_tools.yaml b/.github/workflows/fetch_all_tools.yaml index 2224d125..b99ea875 100644 --- a/.github/workflows/fetch_all_tools.yaml +++ b/.github/workflows/fetch_all_tools.yaml @@ -35,10 +35,11 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install requirement run: python -m pip install -r requirements.txt - - name: Run script + - name: Run script #needs PAT to access other repos run: | - export GITHUB_API_KEY=${{ secrets.GH_API_TOKEN }} bash ./bin/extract_all_tools_stepwise.sh "${{ matrix.subset }}" + env: + GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }} - name: Commit all tools # add or commit any changes in results if there was a change, merge with main and push as bot run: | @@ -60,10 +61,13 @@ jobs: ref: main #pull latest code produced by job 1, not the revision that started the workflow (https://github.com/actions/checkout/issues/439) - uses: actions/setup-python@v5 - name: Install requirement - run: python -m pip install -r requirements.txt + run: | + python -m pip install -r requirements.txt + sudo apt-get install jq - name: Merge all tools run: | #merge files with only one header -> https://stackoverflow.com/questions/16890582/unixmerge-multiple-csv-files-with-same-header-by-keeping-the-header-of-the-firs awk 'FNR==1 && NR!=1{next;}{print}' results/repositories*.list_tools.tsv > results/all_tools.tsv + jq -s '.' results/repositories*.list_tools.json > results/all_tools.json - name: Wordcloud and interactive table run: | bash ./bin/extract_all_tools_downstream.sh @@ -76,4 +80,4 @@ jobs: git add results git status git diff --quiet && git diff --staged --quiet || (git commit -m "fetch all tools bot - step merge") - git push \ No newline at end of file + git push diff --git a/.github/workflows/filter_communities.yaml b/.github/workflows/filter_communities.yaml index 97b6fc3d..e7cc5000 100644 --- a/.github/workflows/filter_communities.yaml +++ b/.github/workflows/filter_communities.yaml @@ -3,10 +3,17 @@ name: Filter community tools on: workflow_dispatch: - # the workflow it triggered when all_tools_tsv is changed + # the workflow it triggered when all tools are fetched + workflow_run: + workflows: ["Fetch all tools"] + types: + - completed + + # the workflow it also triggered when the community definitions are changed push: paths: - - 'results/all_tools.tsv' + - 'data/communities**' + branches: ["main"] # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml index 5ec43248..67d3814b 100644 --- a/.github/workflows/static.yml +++ b/.github/workflows/static.yml @@ -2,11 +2,12 @@ name: Deploy static content to Pages on: - # the workflow is triggered when any of the results are changed - push: - paths: - - 'results/**' + # the workflow it triggered when the tools where filtered + workflow_run: + workflows: ["Filter community tools"] + types: + - completed # Allows you to run this workflow manually from the Actions tab workflow_dispatch: diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..1ef1be31 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,8 @@ +Code of Conduct +=============== + +As part of the Galaxy Community, this project is committed to providing a +welcoming and harassment-free experience for everyone. We therefore expect +participants to abide by our Code of Conduct, which can be found at: + +https://galaxyproject.org/community/coc/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..919ca29b --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2024 Galaxy Project + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index cc8e9bdc..eddaba15 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,16 @@ Galaxy Tool Metadata Extractor This tool automatically collects a table of all available Galaxy tools including their metadata. The created table -can be filtered to only show the tools relevant for a specific community. **Learn [how to add your community](#add-your-community)**. +can be filtered to only show the tools relevant for a specific community. -The tools performs the following steps: +Any Galaxy community can be added to this project and benefit from a dedicated interactive table that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN toturial**. + +The interactive table benefits from EDAM annotations of the tools, this requires, that the tools are annotation via bio.tools. +**Learn [how to improve metadata for Galaxy tools using the bio.tools registry](https://training.galaxyproject.org/training-material//topics/dev/tutorials/tool-annotation/tutorial.html)**. + +# Tool workflows + +The tool performs the following steps: - Parse tool GitHub repository from [Planemo monitor listed](https://github.com/galaxyproject/planemo-monitor) - Check in each repo, their `.shed.yaml` file and filter for categories, such as metagenomics @@ -22,8 +29,6 @@ The tools performs the following steps: - Creates an interactive table for all tools: [All tools](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/) - Creates an interactive table for all registered communities, e.g. [microGalaxy](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/) - - # Usage ## Prepare environment @@ -90,28 +95,30 @@ The script will generate a TSV file with each tool found in the list of GitHub r 1. Run the extraction as explained before 2. (Optional) Create a text file with ToolShed categories for which tools need to be extracted: 1 ToolShed category per row ([example for microbial data analysis](data/microgalaxy/categories)) -3. (Optional) Create a text file with list of tools to exclude: 1 tool id per row ([example for microbial data analysis](data/microgalaxy/tools_to_exclude)) -4. (Optional) Create a text file with list of tools to really keep (already reviewed): 1 tool id per row ([example for microbial data analysis](data/microgalaxy/tools_to_keep)) +3. (Optional) Create a TSV (tabular) file with tool status (1 tool suite per row) as 3 columns: + - ToolShed ids of tool suites (one per line) + - Boolean with True to keep and False to exclude + - Boolean with True if deprecated and False if not + + [Example for microbial data analysis](data/microgalaxy/tools_to_keep_exclude.tsv) + 4. Run the tool extractor script ``` $ python bin/extract_galaxy_tools.py \ - --tools \ - --filtered_tools \ + --tools \ + --ts-filtered-tools + --filtered-tools \ [--categories ] \ - [--excluded ]\ - [--keep ] + [--status ] ``` +## Development +To make a test run of the tool to check its functionalities follow [Usage](#Usage) to set-up the environnement and the API key, then run -## Add your community - -In order to add your community you need to: -- Fork this repository. -- Add a folder for your community in `data/communities`. -- Add at least the file `categories`. -- Add all `categories` that are relevant to initially filter the tools for your community. Possible categories are listed here [Galaxy toolshed](https://toolshed.g2.bx.psu.edu/). -- Make a pull request to add your community. -- The workflow will run every sunday, so on the next monday, your community table should be added to `results/` +```bash +bash ./bin/extract_all_tools_test.sh test.list +``` +This runs the tool, but only parses the test repository [Galaxy-Tool-Metadata-Extractor-Test-Wrapper](https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper) diff --git a/bin/create_interactive_table.py b/bin/create_interactive_table.py index 569bdd2f..d91dd99f 100644 --- a/bin/create_interactive_table.py +++ b/bin/create_interactive_table.py @@ -4,7 +4,7 @@ import pandas as pd -# TODO maybe allow comunities to modify +# TODO maybe allow communities to modify COLUMNS = [ "Expand", "Galaxy wrapper id", @@ -18,25 +18,43 @@ "EDAM topic", "Description", "bio.tool description", + "biii", "Status", "Source", "ToolShed categories", "ToolShed id", "Galaxy wrapper owner", "Galaxy wrapper source", + "Galaxy wrapper parsed folder", ] +COLUMNS_TO_DROP = [ + "Reviewed", + "To keep", +] + + +# COLUMNS_TO_ADD = [ +# "Expand" +# ] + def generate_table( tsv_path: str, template_path: str, output_path: str, ) -> None: - df = pd.read_csv(tsv_path, sep="\t").assign(Expand=lambda df: "").fillna("") + df = pd.read_csv(tsv_path, sep="\t") + df.insert(0, "Expand", None) # the column where the expand button is shown + df = df.fillna("") + if "To keep" in df.columns: df["To keep"] = df["To keep"].replace("", True) df = df.query("`To keep`") - df = df.loc[:, COLUMNS].reindex(columns=COLUMNS) + + df = df.drop(COLUMNS_TO_DROP, axis=1) + + # df = df.loc[:, COLUMNS].reindex(columns=COLUMNS) table = df.to_html(border=0, table_id="dataframe", classes=["display", "nowrap"], index=False) with open(template_path) as template_file: diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh index f4e03534..d8efcd01 100755 --- a/bin/extract_all_tools.sh +++ b/bin/extract_all_tools.sh @@ -5,7 +5,8 @@ mkdir -p 'results/' python bin/extract_galaxy_tools.py \ extractools \ --api $GITHUB_API_KEY \ - --all_tools 'results/all_tools.tsv' + --all-tools 'results/all_tools.tsv' \ + --all-tools-json 'results/all_tools.json' python bin/create_interactive_table.py \ --table "results/all_tools.tsv" \ diff --git a/bin/extract_all_tools_stepwise.sh b/bin/extract_all_tools_stepwise.sh index 7b9cac75..8545fd43 100755 --- a/bin/extract_all_tools_stepwise.sh +++ b/bin/extract_all_tools_stepwise.sh @@ -2,11 +2,25 @@ mkdir -p 'results/' -output="results/${1}_tools.tsv" +tsv_output="results/${1}_tools.tsv" +json_output="results/${1}_tools.json" -python bin/extract_galaxy_tools.py \ +if [[ $1 =~ "01" ]]; then + python bin/extract_galaxy_tools.py \ extractools \ --api $GITHUB_API_KEY \ - --all_tools $output \ - --planemorepository $1 + --all-tools $tsv_output \ + --all-tools-json $json_output \ + --planemo-repository-list $1 +else + python bin/extract_galaxy_tools.py \ + extractools \ + --api $GITHUB_API_KEY \ + --all-tools $tsv_output \ + --all-tools-json $json_output \ + --planemo-repository-list $1 \ + --avoid-extra-repositories +fi + + diff --git a/bin/extract_all_tools_test.sh b/bin/extract_all_tools_test.sh index 9960b9ea..2ba40be5 100755 --- a/bin/extract_all_tools_test.sh +++ b/bin/extract_all_tools_test.sh @@ -2,12 +2,14 @@ mkdir -p 'results/' -output="results/${1}_tools.tsv" +tsv_output="results/${1}_tools.tsv" +json_output="results/${1}_tools.json" python bin/extract_galaxy_tools.py \ extractools \ --api $GITHUB_API_KEY \ - --all_tools $output \ - --planemorepository $1 \ + --all-tools $tsv_output \ + --all-tools-json $json_output \ + --planemo-repository-list $1 \ --test diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py index f26254f8..e71e5525 100644 --- a/bin/extract_galaxy_tools.py +++ b/bin/extract_galaxy_tools.py @@ -2,6 +2,7 @@ import argparse import base64 +import json import sys import time import xml.etree.ElementTree as et @@ -20,8 +21,7 @@ from github import Github from github.ContentFile import ContentFile from github.Repository import Repository -from owlready2 import get_ontology, Thing - +from owlready2 import get_ontology # Config variables BIOTOOLS_API_URL = "https://bio.tools" @@ -31,16 +31,22 @@ "https://usegalaxy.org", "https://usegalaxy.org.au", "https://usegalaxy.eu", + "https://usegalaxy.fr", ] project_path = Path(__file__).resolve().parent.parent # galaxy_tool_extractor folder usage_stats_path = project_path.joinpath("data", "usage_stats") +conf_path = project_path.joinpath("data", "conf.yml") GALAXY_TOOL_STATS = { "No. of tool users (2022-2023) (usegalaxy.eu)": usage_stats_path.joinpath("tool_usage_per_user_2022_23_EU.csv"), "Total tool usage (usegalaxy.eu)": usage_stats_path.joinpath("total_tool_usage_EU.csv"), } +# load the configs globally +with open(conf_path) as f: + configs = yaml.safe_load(f) + def get_last_url_position(toot_id: str) -> str: """ @@ -118,24 +124,26 @@ def get_string_content(cf: ContentFile) -> str: return base64.b64decode(cf.content).decode("utf-8") -def get_tool_github_repositories(g: Github, RepoSelection: Optional[str], run_test: bool) -> List[str]: +def get_tool_github_repositories( + g: Github, repository_list: Optional[str], run_test: bool, add_extra_repositories: bool = True +) -> List[str]: """ Get list of tool GitHub repositories to parse :param g: GitHub instance - :param RepoSelection: The selection to use from the repository (needed to split the process for CI jobs) - :run_test: for CI testing only use one repository + :param repository_list: The selection to use from the repository (needed to split the process for CI jobs) + :param run_test: for testing only parse the repository """ if run_test: - return ["https://github.com/TGAC/earlham-galaxytools"] + return ["https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper"] repo = g.get_user("galaxyproject").get_repo("planemo-monitor") repo_list: List[str] = [] for i in range(1, 5): repo_selection = f"repositories0{i}.list" - if RepoSelection: # only get these repositories - if RepoSelection == repo_selection: + if repository_list: # only get these repositories + if repository_list == repo_selection: repo_f = repo.get_contents(repo_selection) repo_l = get_string_content(repo_f).rstrip() repo_list.extend(repo_l.split("\n")) @@ -144,6 +152,11 @@ def get_tool_github_repositories(g: Github, RepoSelection: Optional[str], run_te repo_l = get_string_content(repo_f).rstrip() repo_list.extend(repo_l.split("\n")) + if ( + add_extra_repositories and "extra-repositories" in configs + ): # add non planemo monitor repositories defined in conf + repo_list = repo_list + configs["extra-repositories"] + print("Parsing repositories from:") for repo in repo_list: print("\t", repo) @@ -182,17 +195,22 @@ def get_shed_attribute(attrib: str, shed_content: Dict[str, Any], empty_value: A return empty_value -def get_biotools(el: et.Element) -> Optional[str]: +def get_xref(el: et.Element, attrib_type: str) -> Optional[str]: """ - Get bio.tools information + Get xref information :param el: Element object + :attrib_type: the type of the xref (e.g.: bio.tools or biii) """ + xrefs = el.find("xrefs") if xrefs is not None: - xref = xrefs.find("xref") - if xref is not None and xref.attrib["type"] == "bio.tools": - return xref.text + xref_items = xrefs.findall("xref") # check all xref items + for xref in xref_items: + if xref is not None and xref.attrib["type"] == attrib_type: + # should not contain any space of linebreak + xref_sanitized = str(xref.text).strip() + return xref_sanitized return None @@ -230,7 +248,7 @@ def check_categories(ts_categories: str, ts_cat: List[str]) -> bool: return True if not ts_categories: return False - ts_cats = ts_categories.split(", ") + ts_cats = ts_categories return bool(set(ts_cat) & set(ts_cats)) @@ -245,11 +263,15 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, """ if tool.type != "dir": return None + + # the folder of the tool is used as Galaxy wrapper id (maybe rather use the .shed.yml name) metadata = { "Galaxy wrapper id": tool.name, "Galaxy tool ids": [], "Description": None, "bio.tool id": None, + "bio.tool ids": set(), # keep track of multi IDs + "biii": None, "bio.tool name": None, "bio.tool description": None, "EDAM operation": [], @@ -259,7 +281,8 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, "ToolShed categories": [], "ToolShed id": None, "Galaxy wrapper owner": None, - "Galaxy wrapper source": None, + "Galaxy wrapper source": None, # this is what it written in the .shed.yml + "Galaxy wrapper parsed folder": None, # this is the actual parsed file "Galaxy wrapper version": None, "Conda id": None, "Conda version": None, @@ -269,6 +292,7 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, shed = repo.get_contents(f"{tool.path}/.shed.yml") except Exception: return None + # parse the .shed.yml else: file_content = get_string_content(shed) yaml_content = yaml.load(file_content, Loader=yaml.FullLoader) @@ -285,9 +309,15 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, metadata["ToolShed categories"] = get_shed_attribute("categories", yaml_content, []) if metadata["ToolShed categories"] is None: metadata["ToolShed categories"] = [] - # find and parse macro file + + # get all files in the folder file_list = repo.get_contents(tool.path) assert isinstance(file_list, list) + + # store the github location where the folder was parsed + metadata["Galaxy wrapper parsed folder"] = tool.html_url + + # find and parse macro file for file in file_list: if "macro" in file.name and file.name.endswith("xml"): file_content = get_string_content(file) @@ -298,10 +328,17 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, metadata["Galaxy wrapper version"] = child.text elif child.attrib["name"] == "requirements": metadata["Conda id"] = get_conda_package(child) - biotools = get_biotools(child) + # bio.tools + biotools = get_xref(child, attrib_type="bio.tools") if biotools is not None: metadata["bio.tool id"] = biotools - # parse XML file and get meta data from there, also tool ids + metadata["bio.tool ids"].add(biotools) + # biii + biii = get_xref(child, attrib_type="biii") + if biii is not None: + metadata["biii"] = biii + + # parse XML file and get meta data from there for file in file_list: if file.name.endswith("xml") and "macro" not in file.name: file_content = get_string_content(file) @@ -324,11 +361,19 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@" ): metadata["Galaxy wrapper version"] = child.text + # bio.tools - if metadata["bio.tool id"] is None: - biotools = get_biotools(root) - if biotools is not None: - metadata["bio.tool id"] = biotools + biotools = get_xref(root, attrib_type="bio.tools") + if biotools is not None: + metadata["bio.tool id"] = biotools + metadata["bio.tool ids"].add(biotools) + + # biii + if metadata["biii"] is None: + biii = get_xref(root, attrib_type="biii") + if biii is not None: + metadata["biii"] = biii + # conda package if metadata["Conda id"] is None: reqs = get_conda_package(root) @@ -337,6 +382,7 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, # tool ids if "id" in root.attrib: metadata["Galaxy tool ids"].append(root.attrib["id"]) + # get latest conda version and compare to the wrapper version if metadata["Conda id"] is not None: r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Conda id"]}') @@ -346,6 +392,7 @@ def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, metadata["Conda version"] = conda_info["latest_version"] if metadata["Conda version"] == metadata["Galaxy wrapper version"]: metadata["Status"] = "Up-to-date" + # get bio.tool information if metadata["bio.tool id"] is not None: r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool id"]}/?format=json') @@ -383,6 +430,7 @@ def parse_tools(repo: Repository) -> List[Dict[str, Any]]: print("No tool folder found", sys.stderr) return [] assert isinstance(repo_tools, list) + tool_folders.append(repo_tools) try: repo_tools = repo.get_contents("tool_collections") @@ -391,6 +439,10 @@ def parse_tools(repo: Repository) -> List[Dict[str, Any]]: else: assert isinstance(repo_tools, list) tool_folders.append(repo_tools) + + # tool_folders will contain a list of all folders in the + # repository named wrappers/tools/tool_collections + # parse folders tools = [] for folder in tool_folders: @@ -400,7 +452,10 @@ def parse_tools(repo: Repository) -> List[Dict[str, Any]]: print("WAITING for 1 hour to retrieve GitHub API request access !!!") print() time.sleep(60 * 60) + # parse tool + # if the folder (tool) has a .shed.yml file run get get_tool_metadata on that folder, + # otherwise go one level down and check if there is a .shed.yml in a subfolder try: repo.get_contents(f"{tool.path}/.shed.yml") except Exception: @@ -495,127 +550,121 @@ def format_list_column(col: pd.Series) -> pd.Series: """ return col.apply(lambda x: ", ".join(str(i) for i in x)) -def process_row(row): -# Remove extra spaces from each column value in the row - cleaned_row = [str(value).strip() for value in row[1:]] # Exclude the first column ('Galaxy tool ids') - - # Convert the cleaned row to a list of EDAM terms using the provided ontology - edam_ontology = get_ontology('https://edamontology.org/EDAM_1.25.owl').load() - - terms = cleaned_row - classes = [edam_ontology.search_one(label=term) for term in terms] - check_classes = [cla for cla in classes if cla is not None] # Remove None values - - new_classes = [] - for cla in check_classes: - try: - # get all subclasses - subclasses = list(cla.subclasses()) - - # check if any of the other classes is a subclass - include_class = True - for subcla in subclasses: - for cla2 in check_classes: - if subcla == cla2: - include_class = False - - # only keep the class if it is not a parent class - if include_class: - new_classes.append(cla) - except Exception as e: - print(f"Error processing class {cla}: {e}") - # convert back to terms, skipping None values - new_terms = [cla.label[0] for cla in new_classes if cla is not None] - - # Include the first column ('Galaxy tool ids') in the returned series - return pd.Series([row[0], ', '.join(new_terms)]) # Combine the new terms with commas - -def process_dataframe(input_df): - # Apply the process_row function to each row in the dataframe - output_df = input_df.apply(process_row, axis=1) - - # Set the header of the output dataframe - output_df.columns = ['Galaxy tool ids', 'EDAM term'] - - return output_df - -def export_tools( +def export_tools_to_json(tools: List[Dict], output_fp: str) -> None: + """ + Export tool metadata to TSV output file + + :param tools: dictionary with tools + :param output_fp: path to output file + """ + with Path(output_fp).open("w") as f: + json.dump(tools, f, default=list, indent=4) + + +def export_tools_to_tsv( tools: List[Dict], output_fp: str, format_list_col: bool = False, add_usage_stats: bool = False ) -> None: """ - Export tool metadata to tsv output file + Export tool metadata to TSV output file :param tools: dictionary with tools :param output_fp: path to output file :param format_list_col: boolean indicating if list columns should be formatting """ - df = pd.DataFrame(tools) + df = pd.DataFrame(tools).sort_values("Galaxy wrapper id") if format_list_col: df["ToolShed categories"] = format_list_column(df["ToolShed categories"]) df["EDAM operation"] = format_list_column(df["EDAM operation"]) df["EDAM topic"] = format_list_column(df["EDAM topic"]) + df["EDAM operation (no superclasses)"] = format_list_column(df["EDAM operation (no superclasses)"]) + df["EDAM topic (no superclasses)"] = format_list_column(df["EDAM topic (no superclasses)"]) + + df["bio.tool ids"] = format_list_column(df["bio.tool ids"]) + # the Galaxy tools need to be formatted for the add_instances_to_table to work df["Galaxy tool ids"] = format_list_column(df["Galaxy tool ids"]) df = add_instances_to_table(df) if add_usage_stats: df = add_usage_stats_for_all_server(df) - - # df_edam = df[df['To keep']==True] - df_edam1 =df[df['EDAM operation'].notna()] - df_edam2 =df[df['EDAM topic'].notna()] - df_operation = pd.concat( [df_edam1['Galaxy tool ids'], df_edam1['EDAM operation'].str.split(',', expand=True).add_prefix('SubColumn')], axis=1 ) - df_topic = pd.concat( [df_edam2['Galaxy tool ids'], df_edam2['EDAM topic'].str.split(',', expand=True).add_prefix('SubColumn')], axis=1 ) - - processed_df_operation = process_dataframe(df_operation) - processed_df_operation = processed_df_operation.rename(columns={'EDAM term': 'EDAM reduced operation'}) - processed_df_topic = process_dataframe(df_topic) - processed_df_topic = processed_df_topic.rename(columns={'EDAM term': 'EDAM reduced topic'}) - - if 'EDAM operation' in df.columns and 'EDAM reduced operation' in processed_df_operation: - # Add the column from processed_df_operation to df with a new name - df['EDAM reduced operation classes'] = df['EDAM operation'] - else: - print("Column 'EDAM operation' not found in one or both dataframes.") - - if 'EDAM topic' in df.columns and 'EDAM reduced topic' in processed_df_topic: - # Add the column from processed_df_topic to df with a new name - df['EDAM reduced topic classes'] = df['EDAM topic'] - else: - print("Column 'EDAM topic' not found in one or both dataframes.") - df.to_csv(output_fp, sep="\t", index=False) + def filter_tools( tools: List[Dict], ts_cat: List[str], - excluded_tools: List[str], - keep_tools: List[str], -) -> List[Dict]: + tool_status: Dict, +) -> tuple: """ Filter tools for specific ToolShed categories and add information if to keep or to exclude :param tools: dictionary with tools and their metadata :param ts_cat: list of ToolShed categories to keep in the extraction - :param excluded_tools: list of tools to skip - :param keep_tools: list of tools to keep + :param tool_status: dictionary with tools and their 2 status: Keep and Deprecated """ + ts_filtered_tools = [] filtered_tools = [] for tool in tools: # filter ToolShed categories and leave function if not in expected categories if check_categories(tool["ToolShed categories"], ts_cat): name = tool["Galaxy wrapper id"] - tool["Reviewed"] = name in keep_tools or name in excluded_tools - tool["To keep"] = None - if name in keep_tools: - tool["To keep"] = True - elif name in excluded_tools: - tool["To keep"] = False - filtered_tools.append(tool) - return filtered_tools + tool["Reviewed"] = name in tool_status + keep = None + deprecated = None + if name in tool_status: + keep = tool_status[name][1] + deprecated = tool_status[name][2] + tool["Deprecated"] = deprecated + if keep: # only add tools that are manually marked as to keep + filtered_tools.append(tool) + tool["To keep"] = keep + ts_filtered_tools.append(tool) + return ts_filtered_tools, filtered_tools + + +def reduce_ontology_terms(terms: List, ontology: Any) -> List: + """ + Reduces a list of Ontology terms, to include only terms that are not super-classes of one of the other terms. + In other terms all classes that have a subclass in the terms are removed. + + :terms: list of terms from that ontology + :ontology: Ontology + """ + + # if list is empty do nothing + if not terms: + return terms + + classes = [ontology.search_one(label=term) for term in terms] + check_classes = [cla for cla in classes if cla is not None] # Remove None values + + new_classes = [] + for cla in check_classes: + try: + # get all subclasses + subclasses = list(cla.subclasses()) + + # check if any of the other classes is a subclass + include_class = True + for subcla in subclasses: + for cla2 in check_classes: + if subcla == cla2: + include_class = False + + # only keep the class if it is not a parent class + if include_class: + new_classes.append(cla) + + except Exception as e: + print(f"Error processing class {cla}: {e}") + + # convert back to terms, skipping None values + new_terms = [cla.label[0] for cla in new_classes if cla is not None] + # print(f"Terms: {len(terms)}, New terms: {len(new_terms)}") + return new_terms if __name__ == "__main__": @@ -626,11 +675,22 @@ def filter_tools( # Extract tools extractools = subparser.add_parser("extractools", help="Extract tools") extractools.add_argument("--api", "-a", required=True, help="GitHub access token") - extractools.add_argument("--all_tools", "-o", required=True, help="Filepath to TSV with all extracted tools") + extractools.add_argument("--all-tools-json", "-j", required=True, help="Filepath to JSON with all extracted tools") + extractools.add_argument("--all-tools", "-o", required=True, help="Filepath to TSV with all extracted tools") extractools.add_argument( - "--planemorepository", "-pr", required=False, help="Repository list to use from the planemo-monitor repository" + "--planemo-repository-list", + "-pr", + required=False, + help="Repository list to use from the planemo-monitor repository", + ) + extractools.add_argument( + "--avoid-extra-repositories", + "-e", + action="store_true", + default=False, + required=False, + help="Do not parse extra repositories in conf file", ) - extractools.add_argument( "--test", "-t", @@ -644,15 +704,21 @@ def filter_tools( filtertools = subparser.add_parser("filtertools", help="Filter tools") filtertools.add_argument( "--tools", + "-i", + required=True, + help="Filepath to JSON with all extracted tools, generated by extractools command", + ) + filtertools.add_argument( + "--ts-filtered-tools", "-t", required=True, - help="Filepath to TSV with all extracted tools, generated by extractools command", + help="Filepath to TSV with tools filtered based on ToolShed category", ) filtertools.add_argument( - "--filtered_tools", + "--filtered-tools", "-f", required=True, - help="Filepath to TSV with filtered tools", + help="Filepath to TSV with tools filtered based on ToolShed category and manual curation", ) filtertools.add_argument( "--categories", @@ -660,14 +726,9 @@ def filter_tools( help="Path to a file with ToolShed category to keep in the extraction (one per line)", ) filtertools.add_argument( - "--exclude", - "-e", - help="Path to a file with ToolShed ids of tools to exclude (one per line)", - ) - filtertools.add_argument( - "--keep", - "-k", - help="Path to a file with ToolShed ids of tools to keep (one per line)", + "--status", + "-s", + help="Path to a TSV file with tool status - 3 columns: ToolShed ids of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not", ) args = parser.parse_args() @@ -675,8 +736,13 @@ def filter_tools( # connect to GitHub g = Github(args.api) # get list of GitHub repositories to parse - repo_list = get_tool_github_repositories(g, args.planemorepository, args.test) - # parse tools in GitHub repositories to extract metada, filter by TS categories and export to output file + repo_list = get_tool_github_repositories( + g=g, + repository_list=args.planemo_repository_list, + run_test=args.test, + add_extra_repositories=not args.avoid_extra_repositories, + ) + # parse tools in GitHub repositories to extract metadata, filter by TS categories and export to output file tools: List[Dict] = [] for r in repo_list: print("Parsing tools from:", (r)) @@ -690,14 +756,26 @@ def filter_tools( f"Error while extracting tools from repo {r}: {e}", file=sys.stderr, ) - export_tools(tools, args.all_tools, format_list_col=True, add_usage_stats=True) + + # add additional information to the List[Dict] object + edam_ontology = get_ontology("https://edamontology.org/EDAM_1.25.owl").load() + + for tool in tools: + tool["EDAM operation (no superclasses)"] = reduce_ontology_terms( + tool["EDAM operation"], ontology=edam_ontology + ) + tool["EDAM topic (no superclasses)"] = reduce_ontology_terms(tool["EDAM topic"], ontology=edam_ontology) + + export_tools_to_json(tools, args.all_tools_json) + export_tools_to_tsv(tools, args.all_tools, format_list_col=True, add_usage_stats=True) elif args.command == "filtertools": - tools = pd.read_csv(Path(args.tools), sep="\t", keep_default_na=False).to_dict("records") + with Path(args.tools).open() as f: + tools = json.load(f) # get categories and tools to exclude categories = read_file(args.categories) - excl_tools = read_file(args.exclude) - keep_tools = read_file(args.keep) + status = pd.read_csv(args.status, sep="\t", index_col=0, header=None).to_dict("index") # filter tool lists - filtered_tools = filter_tools(tools, categories, excl_tools, keep_tools) - export_tools(filtered_tools, args.filtered_tools) + ts_filtered_tools, filtered_tools = filter_tools(tools, categories, status) + export_tools_to_tsv(ts_filtered_tools, args.ts_filtered_tools, format_list_col=True) + export_tools_to_tsv(filtered_tools, args.filtered_tools, format_list_col=True) diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh index 96f52b0c..a0566eef 100755 --- a/bin/get_community_tools.sh +++ b/bin/get_community_tools.sh @@ -7,28 +7,15 @@ for com_data_fp in data/communities/* ; do echo "$community"; - if [[ "$community" == *"microgalaxy"* ]]; then - curl \ - -L \ - "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=1533244711" \ - -o "data/communities/$community/tools_to_keep" - - curl \ - -L \ - "https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hfSg3zu9L4/export?format=tsv&gid=672552331" \ - -o "data/communities/$community/tools_to_exclude" - fi; - - mkdir -p "results/$community" python bin/extract_galaxy_tools.py \ filtertools \ - --tools "results/all_tools.tsv" \ - --filtered_tools "results/$community/tools.tsv" \ + --tools "results/all_tools.json" \ + --ts-filtered-tools "results/$community/tools_filtered_by_ts_categories.tsv" \ + --filtered-tools "results/$community/tools.tsv" \ --categories "data/communities/$community/categories" \ - --exclude "data/communities/$community/tools_to_exclude" \ - --keep "data/communities/$community/tools_to_keep" + --status "data/communities/$community/tool_status.tsv" python bin/create_interactive_table.py \ --table "results/$community/tools.tsv" \ diff --git a/data/communities/imaging/tools_to_exclude b/data/communities/imaging/tool_status.tsv similarity index 100% rename from data/communities/imaging/tools_to_exclude rename to data/communities/imaging/tool_status.tsv diff --git a/data/communities/imaging/tools_to_keep b/data/communities/imaging/tools_to_keep deleted file mode 100644 index e69de29b..00000000 diff --git a/data/communities/microgalaxy/tool_status.tsv b/data/communities/microgalaxy/tool_status.tsv new file mode 100644 index 00000000..ba003585 --- /dev/null +++ b/data/communities/microgalaxy/tool_status.tsv @@ -0,0 +1,773 @@ +abacas TRUE FALSE +abricate TRUE FALSE +abritamr TRUE FALSE +abyss TRUE FALSE +adapter_removal FALSE FALSE +aegean FALSE FALSE +AggregateAlignments FALSE FALSE +aldex2 TRUE FALSE +align_back_trans FALSE FALSE +AlignCluster FALSE FALSE +amplican TRUE FALSE +ampvis2 FALSE FALSE +amrfinderplus TRUE FALSE +ancombc TRUE FALSE +anndata FALSE FALSE +annotatemyids FALSE FALSE +antarna FALSE FALSE +antismash TRUE FALSE +aresite2 FALSE FALSE +arriba FALSE FALSE +art FALSE FALSE +artic TRUE FALSE +assembly-stats FALSE FALSE +assemblystats TRUE FALSE +augustus FALSE FALSE +b2btools FALSE FALSE +bakta TRUE FALSE +bam2mappingstats FALSE FALSE +bamclipper FALSE FALSE +bamhash FALSE FALSE +bamparse FALSE FALSE +bamtools TRUE FALSE +bamtools_filter FALSE FALSE +bamtools_split FALSE FALSE +bamutil FALSE FALSE +bandage TRUE FALSE +barcode_collapse FALSE FALSE +baredsc FALSE FALSE +barrnap 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TRUE FALSE +suite_qiime2__feature_classifier TRUE FALSE +suite_qiime2__feature_table TRUE FALSE +suite_qiime2__fragment_insertion TRUE FALSE +suite_qiime2__longitudinal TRUE FALSE +suite_qiime2__metadata TRUE FALSE +suite_qiime2__phylogeny TRUE FALSE +suite_qiime2__quality_control TRUE FALSE +suite_qiime2__quality_filter TRUE FALSE +suite_qiime2__rescript TRUE FALSE +suite_qiime2__sample_classifier TRUE FALSE +suite_qiime2__taxa TRUE FALSE +suite_qiime2__vsearch TRUE FALSE +suite_qiime2_core TRUE FALSE +suite_qiime2_core__tools TRUE FALSE +suite_snvphyl FALSE FALSE +syndiva FALSE FALSE +t_coffee TRUE FALSE +t2ps TRUE FALSE +t2t_report TRUE FALSE +tapscan FALSE FALSE +tarfast5 FALSE FALSE +targetfinder FALSE FALSE +tasmanian_mismatch FALSE FALSE +taxonomy_filter_refseq FALSE FALSE +taxonomy_krona_chart TRUE FALSE +tb-profiler TRUE FALSE +tbl2gff3 FALSE FALSE +te_finder FALSE FALSE +telescope FALSE FALSE +tetoolkit FALSE FALSE +tetyper FALSE FALSE +tgsgapcloser FALSE FALSE 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FALSE +vsearch TRUE FALSE +vsnp FALSE FALSE +vt FALSE FALSE +wade FALSE FALSE +weather_app FALSE FALSE +weightedaverage FALSE FALSE +windowmasker FALSE FALSE +windowsplitter FALSE FALSE +wtdbg TRUE FALSE +xarray FALSE FALSE +xpore FALSE FALSE +yac_clipper FALSE FALSE +yahs FALSE FALSE +zoo_project_ogc_api_processes FALSE FALSE \ No newline at end of file diff --git a/data/communities/microgalaxy/tools_to_exclude b/data/communities/microgalaxy/tools_to_exclude deleted file mode 100644 index 6f30553a..00000000 --- a/data/communities/microgalaxy/tools_to_exclude +++ /dev/null @@ -1,502 +0,0 @@ -braker -braker3 -helixer -logol -peptimapper -GAFA -blast_parser -gblocks -hcluster_sg -hcluster_sg_parser -miranda -smart_domains -t_coffee -bam2mappingstats -bamclipper -bundle_collections -collapse_collection -combineJSON -combine_tabular_collection -fasta2bed -fasta_extract -fastqc_stats -feht -kaptive -mauve_contig_mover -pangolin -patrist -plasmid_profiler_suite -pseudogenome -quasitools 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-proteomiqon_joinquantpepionswithproteins -proteomiqon_labeledproteinquantification -proteomiqon_labelfreeproteinquantification -proteomiqon_mzmltomzlite -proteomiqon_peptidedb -proteomiqon_peptidespectrummatching -proteomiqon_proteininference -proteomiqon_psmbasedquantification -proteomiqon_psmstatistics -proteore_venn_diagram -psm_validation -pyprophet -pyteomics -quantp -quantwiz_iq -rawtools -sixgill -spectrast2spectrast_irt -spectrast2tsv -translate_bed_sequences -unipept -uniprotxml_downloader -validate_fasta_database -bamparse -blast_to_scaffold -blastparser_and_hits -blastx_to_scaffold -cap3 -deseq2_normalization -fisher_test -gsc_high_dimensions_visualisation -guppy -high_dim_heatmap -mapping_quality_stats -mircounts -oases -probecoverage -rsem -sashimi_plot -small_rna_clusters -small_rna_maps -small_rna_signatures -sr_bowtie -sr_bowtie_dataset_annotation -tarfast5 -xpore -yac_clipper -EMLassemblyline -Ecoregionalization_workflow -champ_blocs -consensus_from_alignments -data_exploration -xarray -gdal -regionalgam -spocc -srs_tools -stoc -vigiechiro -climate-stripes -mean-per-zone -psy-maps -droplet-barcode-plot -fastq_provider -gtf-2-gene-list -fastq_utils -salmon-kallisto-mtx-to-10x -cell-types-analysis -data-hca -data-scxa -dropletutils -garnett -monocle3 -sc3 -scanpy -scater -scmap -scpred -seurat -mzml_validator -consolidate_vcfs -filter_density -filter_stats -filter_vcf -find_repeats -snv_matrix -vcf2snvalignment -verify_map -suite_snvphyl \ No newline at end of file diff --git a/data/communities/microgalaxy/tools_to_keep b/data/communities/microgalaxy/tools_to_keep deleted file mode 100644 index 0e2d8278..00000000 --- a/data/communities/microgalaxy/tools_to_keep +++ /dev/null @@ -1,218 +0,0 @@ -TreeBest -ete -lotus2 -abacas -assemblystats -biohansel -combine_assembly_stats -cryptogenotyper -ectyper -filter_spades_repeats -getmlst -hivtrace -kat_filter -mob_suite -mrbayes -mykrobe_parser -plasmidspades -promer -sistr_cmd -smalt -srst2 -staramr 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-jellyfish -kc-align -khmer -kleborate -kofamscan -kraken_biom -kraken_taxonomy_report -krakentools -krocus -legsta -lineagespot -lorikeet -m6anet -maaslin2 -maker -mapseq -mash -maxbin2 -medaka -megahit -megahit_contig2fastg -megan -meningotype -merqury -meryl -metabat2 -metaeuk -metagenomeseq -metaphlan -minia -miniasm -miniprot -mitos -mlst -mothur -multigsea -multiqc -mykrobe -nanocompore -nanoplot -nanopolishcomp -newick_utils -nextclade -nonpareil -nugen_nudup -orfipy -orthofinder -pharokka -phyloseq -phyml -picrust -picrust2 -plasflow -plasmidfinder -prokka -proteinortho -pycoqc -pygenometracks -qiime_add_on -qiime_core -qualimap -quast -quickmerge -raxml -read_it_and_keep -recentrifuge -roary -rseqc -sarscov2formatter -sarscov2summary -scoary -semibin -seqkit -shovill -smallgenomeutilities -snap -snippy -sonneityping -spades -spotyping -srst2 -structure -taxonomy_krona_chart -tb-profiler -transtermhp -unicycler -usher -valet -vapor -vegan -velvet -velvet_optimiser -vsearch -bamtools -biotradis -kraken -kraken2 -eggnog_mapper -metagene_annotator -PAMPA -obisindicators \ No newline at end of file diff --git a/data/conf.yml b/data/conf.yml new file mode 100644 index 00000000..1e16fb9f --- /dev/null +++ b/data/conf.yml @@ -0,0 +1,2 @@ +extra-repositories: + - https://github.com/qiime2/galaxy-tools diff --git a/docs/publications/BioHackrXiv/annotation.png b/docs/publications/BioHackrXiv/annotation.png new file mode 100644 index 00000000..6664d268 Binary files /dev/null and b/docs/publications/BioHackrXiv/annotation.png differ diff --git a/docs/publications/BioHackrXiv/flowchart.png b/docs/publications/BioHackrXiv/flowchart.png new file mode 100644 index 00000000..40829e66 Binary files /dev/null and b/docs/publications/BioHackrXiv/flowchart.png differ diff --git a/docs/publications/BioHackrXiv/itable.png b/docs/publications/BioHackrXiv/itable.png new file mode 100644 index 00000000..0384af6e Binary files /dev/null and b/docs/publications/BioHackrXiv/itable.png differ diff --git a/docs/publications/BioHackrXiv/paper.bib b/docs/publications/BioHackrXiv/paper.bib new file mode 100644 index 00000000..925be13a --- /dev/null +++ b/docs/publications/BioHackrXiv/paper.bib @@ -0,0 +1,223 @@ +@article{10.1093/nar/gkac247, + author = {{The Galaxy Community}}, + title = "{The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update}", + journal = {Nucleic Acids Research}, + volume = {50}, + number = {W1}, + pages = {W345-W351}, + year = {2022}, + month = {04}, + abstract = "{Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with \\>230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.}", + issn = {0305-1048}, + doi = {10.1093/nar/gkac247}, + url = {https://doi.org/10.1093/nar/gkac247}, + eprint = {https://academic.oup.com/nar/article-pdf/50/W1/W345/45189566/gkac247.pdf}, +} + +@article{rost2016openms, + title={OpenMS: a flexible open-source software platform for mass spectrometry data analysis}, + author={R\"{o}st, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E and Schilling, Oliver and Choudhary, Jyoti S and Malmstr\"{o}m, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver}, + journal={Nature Methods}, + doi={10.1038/nmeth.3959}, + volume={13}, + number={9}, + pages={741--748}, + year={2016}, + publisher={Nature Publishing Group} +} + +@article{10.1128/AEM.01541-09, +author = {Patrick D. Schloss and Sarah L. Westcott and Thomas Ryabin and Justine R. Hall and Martin Hartmann and Emily B. Hollister and Ryan A. Lesniewski and Brian B. Oakley and Donovan H. Parks and Courtney J. Robinson and Jason W. Sahl and Blaz Stres and Gerhard G. Thallinger and David J. Van Horn and Carolyn F. Weber}, +title = {{Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities}}, +journal = {Applied and Environmental Microbiology}, +volume = {75}, +number = {23}, +pages = {7537-7541}, +year = {2009}, +doi = {10.1128/AEM.01541-09}, +URL = {https://journals.asm.org/doi/abs/10.1128/aem.01541-09}, +eprint = {https://journals.asm.org/doi/pdf/10.1128/aem.01541-09}, +abstract = {mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.} +} + +@article{black2021edam, + title={EDAM: The bioscientific data analysis ontology (update 2021)[version 1; not peer reviewed]}, + author={Black, Melissa and Lamothe, Lucie and {Hager Eldakroury} and Kierkegaard, Mads and {Ankita Priya} and Machinda, Anne and Khanduja, Uttam Singh and {Drashti Patoliya} and {Rashika Rathi} and {Tawah Peggy Che Nico} and Umutesi, Gloria and Blankenburg, Claudia and Op, Anita and Chieke, Precious and {Omodolapo Babatunde} and Laurie, Steve and Neumann, Steffen and Schw\"{a}mmle, Veit and Kuzmin, Ivan and Hunter, Chris and Karr, Jonathan and Ison, Jon and Gaignard, Alban and Brancotte, Bryan and Ménager, Hervé and {Matúš Kalaš}}, + year={2022}, + doi={10.7490/f1000research.1118900.1}, + journal={F1000Research}, + publisher={F1000} +} + +@article{biotoolsSchema, + author = {Ison, Jon and Ienasescu, Hans and Rydza, Emil and Chmura, Piotr and Rapacki, Kristoffer and Gaignard, Alban and Schwämmle, Veit and van Helden, Jacques and Kala{\v{s}}, Mat{\'u}{\v{s}} and M{\'e}nager, Herv{\'e}}, + title = "{biotoolsSchema: a formalized schema for bioinformatics software description}", + journal = {GigaScience}, + volume = {10}, + number = {1}, + pages = {giaa157}, + year = {2021}, + month = {01}, + issn = {2047-217X}, + doi = {10.1093/gigascience/giaa157}, + url = {https://doi.org/10.1093/gigascience/giaa157}, + eprint = {https://academic.oup.com/gigascience/article-pdf/10/1/giaa157/36126150/giaa157.pdf}, +} + +@article{Ison2019, + title = {The bio.tools registry of software tools and data resources for the life sciences}, + volume = {20}, + ISSN = {1474-760X}, + url = {http://doi.org/10.1186/s13059-019-1772-6}, + DOI = {10.1186/s13059-019-1772-6}, + number = {1}, + journal = {Genome Biology}, + publisher = {Springer Science and Business Media LLC}, + author = {Ison, Jon and Ienasescu, Hans and Chmura, Piotr and Rydza, Emil and M{\'e}nager, Herv{\'e} and Kala{\v{s}}, Mat{\'u}{\v{s}} and Schw\"{a}mmle, Veit and Gr\"{u}ning, Bj\"{o}rn and Beard, Niall and Lopez, Rodrigo and Duvaud, Severine and Stockinger, Heinz and Persson, Bengt and Vařeková, Radka Svobodová and Raček, Tomáš and Vondrášek, Jiří and Peterson, Hedi and Salumets, Ahto and Jonassen, Inge and Hooft, Rob and Nyr\"{o}nen, Tommi and Valencia, Alfonso and Capella, Salvador and Gelpí, Josep and Zambelli, Federico and Savakis, Babis and Leskošek, Brane and Rapacki, Kristoffer and Blanchet, Christophe and Jimenez, Rafael and Oliveira, Arlindo and Vriend, Gert and Collin, Olivier and van Helden, Jacques and Løngreen, Peter and Brunak, Søren}, + year = {2019}, + month = aug +} + +@article {Bray2022.03.13.483965, + author = {Simon Bray and Matthias Bernt and Nicola Soranzo and Marius van den Beek and B{\'e}r{\'e}nice Batut and Helena Rasche and Martin {\v C}ech and Peter Cock and Anton Nekrutenko and Bj{\"o}rn Gr{\"u}ning and John Chilton}, + title = {Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses}, + elocation-id = {2022.03.13.483965}, + year = {2022}, + doi = {10.1101/2022.03.13.483965}, + publisher = {Cold Spring Harbor Laboratory}, + abstract = {There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo{\textquoteright}s implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.Competing Interest StatementThe authors have declared no competing interest.}, + URL = {https://www.biorxiv.org/content/early/2022/03/14/2022.03.13.483965}, + eprint = {https://www.biorxiv.org/content/early/2022/03/14/2022.03.13.483965.full.pdf}, + journal = {bioRxiv} +} + +@misc{datatables, + title = {{DataTables} {\textbar} {Table} plug-in for {jQuery}}, + url = {https://datatables.net/}, + urldate = {2023-11-28}, +} + +@misc{conda, + title = {Anaconda Software Distribution}, + url = {https://anaconda.com}, + urldate = {2016-11-01} +} + +@article{edamBrowser, doi = {10.21105/joss.00698}, url = {https://doi.org/10.21105/joss.00698}, year = {2018}, publisher = {The Open Journal}, volume = {3}, number = {27}, pages = {698}, author = {Bryan Brancotte and Christophe Blanchet and Hervé Ménager}, title = {A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.}, journal = {Journal of Open Source Software} } + +@misc{edamBrowserCode, + doi = {10.5281/zenodo.5808818}, + url = {https://zenodo.org/doi/10.5281/zenodo.5808818}, + author = {Eldakroury, Hager and Dhamija, Sakshi and Rathi, Rashika and Patoliya, Drashti and Nkwuda, Sunday Cletus and Singh, Guneet and Yadav, Pooja and D'oleo, Kelly and Cherop, Marlene and Che Nico, Tawah Peggy and Kalaš, Matúš and Ménager, Hervé and Brancotte, Bryan}, + keywords = {Ontology browser, Biosciences, Imaging, Machine learning, Domain ontology, EDAM}, + language = {en}, + title = {{EDAM Browser 2.0.0: Browsing multiple versions of EDAM}}, + publisher = {Zenodo}, + year = {2021}, + copyright = {MIT License} +} + +@article{batut_community-driven_2018, + title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}}, + volume = {6}, + issn = {24054712}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2405471218302308}, + doi = {10.1016/j.cels.2018.05.012}, + language = {en}, + number = {6}, + urldate = {2024-02-26}, + journal = {Cell Systems}, + author = {Batut, Bérénice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Guéguen, Loraine and Čech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivière, Delphine and Le Corguillé, Gildas and Manke, Thomas and Mareuil, Fabien and Ramírez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Grüning, Björn}, + month = jun, + year = {2018}, + pages = {752--758.e1}, +} + +@Article{elixirBiodiversity, +AUTHOR = { Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Heil, KF and Hughes, GM and Jermiin, LS and Kala\v{s}, M and Lanfear, J and Pafilis, E and Papageorgiou, AC and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T}, +TITLE = {{The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity [version 1; peer review: 1 approved with reservations, 1 not approved]}}, +JOURNAL = {F1000Research}, +VOLUME = {12}, +YEAR = {2023}, +NUMBER = {499}, +DOI = {10.12688/f1000research.133724.1} +} + +@misc{RSEc, + doi = {10.7490/f1000research.1119604.1}, + url = {https://f1000research.com/slides/12-1044}, + author = {Ienasescu, Hans and Capella-Gutiérrez, Salvador and Coppens, Frederik and Fernández, José María and Gaignard, Alban and Goble, Carole and Gr\"{u}ning, Bj\"{o}rn and Gustafsson, Johan and Gelpi, Josep Ll and Harrow, Jennifer and Manos, Steven and Miura, Kota and M\"{o}ller, Steffen and Owen, Stuart and Paul-Gilloteaux, Perrine and Peterson, Hedi and Pitoulias, Manthos and Tedds, Jonathan and Repchevsky, Dmitri and Zambelli, Federico and Zharkov, Oleg and Kala\v{s}, Mat\'{u}\v{s} and Ménager, Hervé}, + title = {The ELIXIR research software ecosystem: an open software metadata commons (BOSC track) [version 1; not peer reviewed]}, + publisher = {F1000 Research}, + year = {2023} +} + +@article{bioimageWorkflows, + title = {Bioimage analysis workflows: community resources to navigate through a complex ecosystem}, + volume = {10}, + ISSN = {2046-1402}, + url = {https://doi.org/10.12688/f1000research.52569.1}, + DOI = {10.12688/f1000research.52569.1}, + journal = {F1000Research}, + publisher = {F1000 Research Ltd}, + author = {Paul-Gilloteaux, Perrine and Tosi, Sébastien and Hériché, Jean-Karim and Gaignard, Alban and Ménager, Hervé and Marée, Raphaël and Baecker, Volker and Klemm, Anna and Kalaš, Matúš and Zhang, Chong and Miura, Kota and Colombelli, Julien}, + year = {2021}, + month = apr, + pages = {320} +} + +@article{blankenberg2014dissemination, + title={{Dissemination of scientific software with Galaxy ToolShed}}, + author={Blankenberg, Daniel and Von Kuster, Gregory and Bouvier, Emil and Baker, Dannon and Afgan, Enis and Stoler, Nicholas and Galaxy Team and Taylor, James and Nekrutenko, Anton}, + journal={Genome Biology}, + volume={15}, + pages={1--3}, + year={2014}, + publisher={Springer} +} + +@misc{dev_community_tool_table, + author = {Bérénice Batut}, + title = {{Creation of an interactive Galaxy tools table for your community (Galaxy Training Materials)}}, + year = {2024}, + url = {https://training.galaxyproject.org/training-material/topics/dev/tutorials/community-tool-table/tutorial.html}, + note = {Online; accessed Thu Mar 14 2024} +} + +@article{Hiltemann_2023, + doi = {10.1371/journal.pcbi.1010752}, + url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752}, + year = 2023, + month = {jan}, + publisher = {Public Library of Science ({PLoS})}, + volume = {19}, + number = {1}, + pages = {e1010752}, + author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, + editor = {Francis Ouellette}, + title = {{Galaxy Training: A powerful framework for teaching!}}, + journal = {PLoS Computational Biology} +} + +@misc{dev_tool_annotation, + author = {Bérénice Batut and Johan Gustafsson and Paul Zierep}, + title = {{Adding and updating best practice metadata for Galaxy tools using the bio.tools registry (Galaxy Training Materials)}}, + year = {2024}, + url = {https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-annotation/tutorial.html}, + note = {Online; accessed Thu Mar 14 2024} +} + +@article{Bolyen2019, + title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2}, + volume = {37}, + ISSN = {1546-1696}, + url = {http://dx.doi.org/10.1038/s41587-019-0209-9}, + DOI = {10.1038/s41587-019-0209-9}, + number = {8}, + journal = {Nature Biotechnology}, + publisher = {Springer Science and Business Media LLC}, + author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R. and Bokulich, Nicholas A. and Abnet, Christian C. and Al-Ghalith, Gabriel A. and Alexander, Harriet and Alm, Eric J. and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E. and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J. and Brown, C. Titus and Callahan, Benjamin J. and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily K. and Da Silva, Ricardo and Diener, Christian and Dorrestein, Pieter C. and Douglas, Gavin M. and Durall, Daniel M. and Duvallet, Claire and Edwardson, Christian F. and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M. and Gibbons, Sean M. and Gibson, Deanna L. and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A. and Janssen, Stefan and Jarmusch, Alan K. and Jiang, Lingjing and Kaehler, Benjamin D. and Kang, Kyo Bin and Keefe, Christopher R. and Keim, Paul and Kelley, Scott T. and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G. I. and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D. and McDonald, Daniel and McIver, Lauren J. and Melnik, Alexey V. and Metcalf, Jessica L. and Morgan, Sydney C. and Morton, Jamie T. and Naimey, Ahmad Turan and Navas-Molina, Jose A. and Nothias, Louis Felix and Orchanian, Stephanie B. and Pearson, Talima and Peoples, Samuel L. and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S. and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R. and Swafford, Austin D. and Thompson, Luke R. and Torres, Pedro J. and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J. and Ul-Hasan, Sabah and van der Hooft, Justin J. J. and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C. and Williamson, Charles H. D. and Willis, Amy D. and Xu, Zhenjiang Zech and Zaneveld, Jesse R. and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J. Gregory}, + year = {2019}, + month = jul, + pages = {852–857} +} diff --git a/docs/publications/BioHackrXiv/paper.md b/docs/publications/BioHackrXiv/paper.md new file mode 100644 index 00000000..55e8f67e --- /dev/null +++ b/docs/publications/BioHackrXiv/paper.md @@ -0,0 +1,228 @@ +--- +title: 'How to increase the findability, visibility, and impact of Galaxy tools for your scientific community' +title_short: 'BH23EU project 25: Finding Galaxy tools' +tags: + - Findability + - Galaxy + - Community-specific Galaxy tools + - Tools + - EDAM + - bio.tools + - Metadata +authors: + - name: Paul Zierep + orcid: 0000-0003-2982-388X + affiliation: 1, a + - name: Bérénice Batut + orcid: 0000-0001-9852-1987 + affiliation: 1, 2, a + - name: Matúš Kalaš + orcid: 0000-0002-1509-4981 + affiliation: 3 + - name: Tunc Kayikcioglu + orcid: 0000-0003-2205-8062 + affiliation: 1 + - name: Engy Nasr + orcid: 0000-0001-9047-4215 + affiliation: 1 + - name: Nicola Soranzo + orcid: 0000-0003-3627-5340 + affiliation: 4 + - name: Wai Cheng Thang + orchid: 0000-0002-1480-3563 + affiliation: 5, 6 + - name: Joseph Wang + orcid: + affiliation: 7 + - name: Ove Johan Ragnar Gustafsson + orcid: 0000-0002-2977-5032 + affiliation: 8 +affiliations: + - name: Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany + index: 1 + - name: Institut Français de Bioinformatique, CNRS UAR 3601, Évry, France & Mésocentre Clermont-Auvergne, Université Clermont Auvergne, Aubiere, France + index: 2 + - name: Department of Informatics, University of Bergen, Norway; and ELIXIR Norway + index: 3 + - name: Earlham Institute, Norwich Research Park, Norwich, UK + index: 4 + - name: Queensland Cyber Infrastructure Foundation (QCIF), Australia + index: 5 + - name: Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia + index: 6 + - name: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia + index: 7 + - name: Australian BioCommons, University of Melbourne, Melbourne, Victoria, Australia + index: 8 + - name: These authors contributed equally to this work + index: a +date: 23 February 2024 +bibliography: paper.bib +event: BH23EU +biohackathon_name: "BioHackathon Europe 2023" +biohackathon_url: "https://biohackathon-europe.org/" +biohackathon_location: "Barcelona, Spain, 2023" +group: Project 25 - Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific communities +git_url: https://github.com/galaxyproject/galaxy_tool_metadata_extractor/tree/e604ffd9866f9c32f797ceee45062b4d6f2a1513/docs/publications/BioHackrXiv +authors_short: Paul Zierep, Bérénice Batut, \emph{et al.} +--- + + +# Introduction or Background + +Galaxy [@citesAsAuthority:10.1093/nar/gkac247] is a web-based analysis platform offering almost 10,000 different tools, which are developed in various GitHub repositories. +Furthermore, the Galaxy community embraces granular implementation of software tools as sub-modules. +In practice, this means that tool suites are separated into sets of Galaxy tools, also known as Galaxy wrappers, that contain the functionality of a corresponding sub-component. +Some key examples of tool suites include [QIIME 2](https://bio.tools/qiime2) [@citesAsAuthority:Bolyen2019] and [OpenMS](https://bio.tools/openms) [@citesAsAuthority:rost2016openms], which translate to tens and even hundreds of Galaxy tools. +While granularity supports the composability of tools into diverse purpose-specific workflows, this decentralised development and modular architecture can make it difficult for Galaxy users to find and use tools. +It may also result in Galaxy tool-wrapper developers duplicating efforts by simultaneously wrapping the same software. +This is further complicated by the scarcity of tool metadata, which prevents filtering of tools as relevant for a specific scientific community or domain, and makes it impossible to employ advanced filtering by ontology terms like the ones from EDAM [@citesAsAuthority:black2021edam]. +The final challenge is also an opportunity: the global and cross-domain nature of Galaxy means that it is a big community. +Solving the visibility of tools across this "ecosystem", and the resulting benefits, are far-reaching for the global collaborative development of data-analysis tools and workflows. + +To provide the scientific community with a comprehensive list of annotated Galaxy tools, +we developed a pipeline at the [ELIXIR BioHackathon Europe 2023](https://2023.biohackathon-europe.org) that collects Galaxy wrappers from a list of GitHub repositories and automatically extracts their metadata (including Conda version [@citesAsAuthority:conda], bio.tools identifier [@citesAsAuthority:biotoolsSchema][@usesDataFrom:Ison2019], BIII identifier [@citesAsAuthority:bioimageWorkflows], and EDAM annotations). +The workflow also queries the availability of the tools from the three main Galaxy servers (usegalaxy.*) as well as usage statistics from [usegalaxy.eu](https://usegalaxy.eu) (Note: the other main Galaxy servers, [usegalaxy.org](https://usagalaxy.org) and [usegalaxy.org.au](https://usagalaxy.org.au), will be queried for usage statistics in coming updates). + +Crucially, the pipeline can filter its inputs to only include tools that are relevant to a specific research community. +Based on the selected filters, a community-specific interactive table is generated that can be embedded, e.g. into the respective [Galaxy Hub](https://galaxyproject.org/) webpage or [Galaxy subdomain](https://galaxyproject.org/eu/subdomains/). +This table allows further filtering and searching for fine-grained tool selection. +The pipeline is fully automated and executes weekly. +Any scientific community can apply the pipeline to create a table specific to their needs. + +An interactive table that presents metadata is only as useful as the metadata annotations it is capturing. +To improve the metadata coverage for the interactive table, the project also directly addressed the quality of tool annotations in bio.tools for the [microGalaxy community](https://galaxyproject.org/community/sig/microbial/): +a community with a focus on tools related to microbial research. + +Annotation guidelines were established for this purpose, the process of updating Galaxy tool wrappers to include bio.tools identifiers was started and the outcome of these activities was evaluated using a crowdsourced approach. During the BioHackathon Europe 2023 week, the annotation practices were applied to the tools selected from the microGalaxy community. +This effort allowed the team to connect more than 50 tools to their respective bio.tools entry, update the registry entry, and collectively peer-review the results. + +The established pipeline and the annotation guidelines can support any scientific community to make their Galaxy tools more findable, visible, comparable, understandable, and accessible. +Here, we describe the methods and processes that resulted from this project and highlight how this will now allow the microGalaxy community to confidently navigate an ever-expanding landscape of research software in the Galaxy framework. + + +# Methods + +## Domain-specific interactive tools table + +To create the domain-specific interactive tools table, Galaxy tool-wrapper suites are first parsed from across multiple GitHub repositories. +In effect, the repositories monitored by the planemo-monitor [@citesAsAuthority:Bray2022.03.13.483965] are scraped using a custom script. +The planemo-monitor is part of the Galaxy tool-update infrastructure and keeps track of the most up-to-date tool development repositories. + +Metadata is extracted from each parsed tool-wrapper suite. +This includes wrapper suite ID, scientific category, Bioconda dependency, and a repository URL from bio.tools. +As a tool suite can be composed of multiple individual tools, the tool IDs for each tool are also extracted. +The bio.tools reference is used to request metadata annotations via the bio.tools API, including bio.tools description and functionality annotation using EDAM ontology concepts [@usesDataFrom:black2021edam]. +The latest Conda package version is retrieved via the Bioconda API and compared to the Galaxy tool version to determine the tool’s update state (i.e. to update, or no update required). + +The Galaxy API is used to query if each tool is installed on one of the three UseGalaxy servers ([usegalaxy.eu](https://usegalaxy.eu/), [usegalaxy.org](https://usegalaxy.org/), [usegalaxy.org.au](https://usegalaxy.org.au/)). Furthermore, the tool usage statistics can be retrieved from an SQL query that needs to be executed by Galaxy administrators. +The query used in the current implementation shows the overall tool usage as well as how many users executed a tool in the last 2 years on the European server ([usegalaxy.eu](https://usegalaxy.eu/)). + +The output of the pipeline is a table that combines Galaxy wrappers with their metadata. +The complete table can then be filtered to include only tools with relevance for specific communities. +The initial filtering step is based on the scientific category, which is defined for every Galaxy tool wrapper. +These categories are high-level and cannot distinguish between specific tool functions. +However, they allow for the isolation of a subgroup of the initial table for further curation. +The filtered table can then be manually curated by community curators. +This curation step involves annotating which of the extracted tools should be kept in the final table. +Curators can use the EDAM annotations and tool descriptions to assist with this curation step. +The `to keep` labels for each tool are stored to reduce the replication of effort even further. +The practical outcome is that for repeat executions of the workflow, only new tools require curation. + +The curated tools are transformed into an interactive web table using the data tables framework[@datatables]. +The table is hosted on GitHub and deployed via GitHub pages for each community. +This implementation enables complex queries and filtering without the need for a database backend. +The table can be embedded in any website via an iframe: examples include the Galaxy community [Hub page for microGalaxy](https://galaxyproject.org/community/sig/microbial#tools) or the [microGalaxy subdomain](https://microgalaxy.usegalaxy.eu/). +Furthermore, a word cloud based on the usage statistics of the tools is created. + +The workflow is run weekly via GitHub Actions continuous integration, providing an up-to-date table for each community. +The usage of an iframe enables updates for the table to propagate automatically to any website where it is deployed. + +Any Galaxy community can use the pipeline by adding a folder in the [project GitHub repository](https://github.com/galaxyproject/galaxy_tool_extractor/). +To initialise the pipeline for a new community you need to add a new subfolder of `data/communities/` , and inside it add a file called 'categories' with a list of Galaxy ToolShed [@citesAsAuthority:blankenberg2014dissemination] categories. +Additionally, tools that should be excluded or included after filtering, can be added to respective files as well. +A working example of the community configuration files can be found in the folder for the microGalaxy community. + +![Workflow of the Galaxy tool metadata extractor pipeline. Tool wrappers are parsed from different repositories and additional metadata is retrieved from bio.tools, Bioconda, and the main public Galaxy servers. Upon filtering and manual curation of the data for specific scientific communities, the data is transformed into interactive web tables and a tool usage statistics-based word cloud, that can be integrated into any website. \label{metadata_extractor_pipeline}](./flowchart.png) + + +## Annotation workflow + +The annotation process begins by selecting a tool from a Galaxy community. +This step can make use of the interactive table created by the Galaxy tool extractor scripts presented above. +A curator then needs to visit the development repository of the Galaxy tool wrapper and search the XML file for a bio.tools xref snippet (Figure \ref{xref_snippet}). + +![xref snippet example for a Galaxy tool wrapper that contains the tool Racon. \label{xref_snippet}](./xref.png) + +bio.tools is then checked to confirm that a bio.tools identifier does, or does not, exist. +The reason for this is that even if a bio.tools identifier exists in a tool wrapper, it may not necessarily exist in bio.tools. +This is an observation based on real-world annotation errors and serves as a useful supporting step to improve Galaxy wrapper annotations and the completeness of the bio.tools registry. +In addition, if a bio.tools identifier is not included in the wrapper, this does not mean that there is not a bio.tools identifier available in the registry. + +There are then two curation paths to choose from, depending on whether a bio.tools identifier exists in the XML wrapper. In both cases, if no bio.tools entry exists, a new entry should be created and updated using the bio.tools wizard. The creation and update of an entry includes adding concepts from the EDAM ontology. This annotation process can be simplified through the use of [EDAM Browser](https://edamontology.github.io/edam-browser/) [@citesAsAuthority:edamBrowser][@citesAsAuthority:edamBrowserCode]. + +In the case where no bio.tools identifier exists in the Galaxy XML wrapper, the development repository needs to be forked and a new branch created. +A new xref snippet can then be added, and a pull request opened against the original repository. + +Figure \ref{annotation_workflow} shows a step-by-step breakdown of the above process. + +![Step-by-step workflow for systematically improving metadata annotations across bio.tools registry entries and Galaxy tool wrappers. After selecting a Galaxy tool and checking for the presence of a bio.tools ID in its XML file, a curator needs to review bio.tools, create a new bio.tools entry (if needed), and then ensure that both this entry and the Galaxy tool XML file are up-to-date. Updating bio.tools makes use of the registry wizard, and updating a Galaxy tool wrapper to include a bio.tools xref snippet requires a pull request against the development repository. \label{annotation_workflow}](./annotation.png) + + +# Outcomes and results + +There were multiple concrete outcomes from this BioHackathon project, including the ability to create interactive Galaxy tools tables as needed for scientific communities, a process for updating bio.tools, in-development Galaxy Training Network (GTN) tutorials [@citesAsAuthority:batut_community-driven_2018] describing this process, and an update to the [Galaxy IUC](https://galaxyproject.org/iuc/) tool wrapping [standards](https://galaxy-iuc-standards.readthedocs.io/en/latest/index.html). +These are described in more detail below. + + +## Prototype interactive table for Galaxy communities + +The described workflow for the Galaxy tool metadata extractor (see Figure \ref{metadata_extractor_pipeline}) was successfully implemented ([GitHub repository](https://github.com/galaxyproject/galaxy_tool_extractor)) and could extract more than 1,300 Galaxy tool suites (see the [GitHub repository pages](https://galaxyproject.github.io/galaxy_tool_metadata_extractor) for an up-to-date table). +Of those tool suites, only 267 had a bio.tools identifier, which highlights the importance of performing the annotation process in parallel and complementing the tools with additional metadata. +An example view of the created interactive table is shown in Figure \ref{web_table}. +As mentioned above, the filtered table for the microGalaxy community has already been embedded in the [Hub page for microGalaxy](https://galaxyproject.org/community/sig/microbial#tools), as well as the dedicated [microGalaxy subdomain](https://microgalaxy.usegalaxy.eu/). +The process for creating a new interactive table for a community is currently being transformed into a GTN tutorial. + +![Screenshot of the interactive web table. The table provides comprehensive metadata for all Galaxy wrappers of a specific community and allows for custom searches based on logic filters over all columns. In the shown example, the user queries for all up-to-date tools that are annotated with an EDAM operation that includes "assembly". \label{web_table}](./itable.png) + + +## bio.tools and EDAM annotations for microGalaxy community + +During the week of the BioHackathon, the microGalaxy community executed the annotation workflow as described in the Methods section (see also Figure \ref{annotation_workflow}). +The initial filtered tool table of the microGalaxy included 218 tool suites, of which 61 had corresponding bio.tools identifiers. +The progress of the work was tracked using a GitHub project board. +After the annotation process, the number of tools with bio.tools annotations was increased to 107. +The added annotations for each respective bio.tools entry were also collectively reviewed by the team. +A rerun of the Galaxy tool metadata extractor pipeline collected the additional information, and the metadata is now included in the interactive microGalaxy tool table. + + +## Training materials and updates to standards + +To provide the Galaxy research communities with simple and straightforward guide to annotating their respective tool stacks, the described work has been converted into two GTN tutorials: + +- [Adding and updating best practice metadata for Galaxy tools using the bio.tools registry](https://gxy.io/GTN:T00421) [@citesAsAuthority:dev_tool_annotation] +- [Creation of an interactive Galaxy tools table for your community](https://training.galaxyproject.org/training-material/topics/dev/tutorials/community-tool-table/tutorial.html) [@citesAsAuthority:dev_community_tool_table] + +The guidelines created were also used to update the [best practices for creating Galaxy tools of the IUC repository](https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html). + + +# Conclusion and outlook + +The project was able to successfully meet its aim of creating reusable prototypes and processes that make the richness of the Galaxy tools ecosystem more discoverable and understandable. +Central to this work was the Galaxy tool metadata extractor pipeline, which is currently generating comprehensive and interactive tabular summaries of Galaxy tools for the [microbial data](https://galaxyproject.org/community/sig/microbial/) and [image analysis](https://galaxyproject.org/use/imaging/) communities within Galaxy (with EU BioHackathon 2023 [Project 16](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/16)). The metadata extractor can be reused by any Galaxy group or community. For example, the [biodiversity and ecology](https://galaxyproject.org/use/ecology/) community will employ this pipeline in the near future [@citesAsAuthority:elixirBiodiversity]. +The generated tabular tool summary provides valuable information that extends beyond the use case of listing community tools. Therefore, an integration with the [Research Software Ecosystem (RSEc)](https://github.com/research-software-ecosystem/content) [@citesAsAuthority:RSEc] is currently being worked on. +Various updates of the Galaxy tool metadata extractor pipeline are also envisioned, such as the integration of comprehensive usage statistics for all large Galaxy servers, additional bio.tools metadata, and a user-friendly integration of manual curation steps. + +A set of updates to standards and processes was also created. +These will support the ongoing growth of the metadata hosted by the interactive tables: primarily by helping communities to maintain and extend the annotations of Galaxy tool wrappers, and the bio.tools ecosystem on which these wrapper annotations depend. + + +# Acknowledgements + +This work was developed as part of BioHackathon Europe 2023. +This work was supported by [ELIXIR](https://elixir-europe.org), the research infrastructure for life science data. +This work was supported by the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia funding. + + +# References + diff --git a/docs/publications/BioHackrXiv/template.md b/docs/publications/BioHackrXiv/template.md new file mode 100644 index 00000000..ce5c09e9 --- /dev/null +++ b/docs/publications/BioHackrXiv/template.md @@ -0,0 +1,83 @@ +--- +title: 'BioHackrXiv template' +tags: + - replace with your own keywords + - at least 3 is recommended +authors: + - name: First Last + orcid: 0000-0000-0000-0000 + affiliation: 1 + - name: Second Last + orcid: 0000-0000-0000-0000 + affiliation: 2 + +affiliations: + - name: Institution 1, address, city, country + index: 1 + - name: Institution 1, address, city, country + index: 2 +date: 01 January 2020 +bibliography: paper.bib +authors_short: Last et al. (2021) BioHackrXiv template +group: BioHackrXiv +event: BioHackathon Europe 2021 +--- + +# Introduction or Background + +Add to this section a couple of paragraphs introducing the work done dring the BioHackathon, CodeFest, VoCamp or Sprint event. Please add references whenever needed, for instance [@Katayama:2010]. + +Please separate paragraphs with a double line. + +## Subsection level 2 + +Please keep sections to a maximum of three levels, even better if only two levels. + +### Subsection level 3 + +Please keep sections to a maximum of three levels. + +## Tables, figures and so on + +Please remember to introduce tables (see Table 1) before they appear on the document. We recommend to center tables, formulas and figure but not the corresponding captions. Feel free to modify the table style as it better suits to your data. + +Table 1 +| Header 1 | Header 2 | +| -------- | -------- | +| item 1 | item 2 | +| item 3 | item 4 | + +Remember to introduce figures (see Figure 1) before they appear on the document. + +![BioHackrXiv logo](./biohackrxiv.png) + +Figure 1. A figure corresponding to the logo of our BioHackrXiv preprint. + +# Other main section on your manuscript level 1 + +Feel free to use numbered lists or bullet points as you need. +* Item 1 +* Item 2 + +# Discussion and/or Conclusion + +We recommend to include some discussion or conclusion about your work. Feel free to modify the section title as it fits better to your manuscript. + +# Future work + +And maybe you want to add a sentence or two on how you plan to continue. Please keep reading to learn about citations and references. + +For citations of references, we prefer the use of parenthesis, last name and year. If you use a citation manager, Elsevier – Harvard or American Psychological Association (APA) will work. If you are referencing web pages, software or so, please do so in the same way. Whenever possible, add authors and year. We have included a couple of citations along this document for you to get the idea. Please remember to always add DOI whenever available, if not possible, please provide alternative URLs. You will end up with an alphabetical order list by authors’ last name. + +# Jupyter notebooks, GitHub repositories and data repositories + +* Please add a list here +* Make sure you let us know which of these correspond to Jupyter notebooks. Although not supported yet, we plan to add features for them +* And remember, software and data need a license for them to be used by others, no license means no clear rules so nobody could legally use a non-licensed research object, whatever that object is + +# Acknowledgements +Please always remember to acknowledge the BioHackathon, CodeFest, VoCamp, Sprint or similar where this work was (partially) developed. + +# References + +Leave thise section blank, create a paper.bib with all your references. \ No newline at end of file diff --git a/docs/publications/BioHackrXiv/xref.png b/docs/publications/BioHackrXiv/xref.png new file mode 100644 index 00000000..7bce36c3 Binary files /dev/null and b/docs/publications/BioHackrXiv/xref.png differ diff --git a/docs/publications/microgalaxy_annotation_hackathon/microGalaxy_tool_metadata_progress.png b/docs/publications/microgalaxy_annotation_hackathon/microGalaxy_tool_metadata_progress.png new file mode 100644 index 00000000..5ca10c0c Binary files /dev/null and b/docs/publications/microgalaxy_annotation_hackathon/microGalaxy_tool_metadata_progress.png differ diff --git a/docs/publications/microgalaxy_annotation_hackathon/paper.bib b/docs/publications/microgalaxy_annotation_hackathon/paper.bib new file mode 100644 index 00000000..9e293f52 --- /dev/null +++ b/docs/publications/microgalaxy_annotation_hackathon/paper.bib @@ -0,0 +1,170 @@ +@article{10.1093/nar/gkac247, + author = {{The Galaxy Community}}, + title = "{The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update}", + journal = {Nucleic Acids Research}, + volume = {50}, + number = {W1}, + pages = {W345-W351}, + year = {2022}, + month = {04}, + abstract = "{Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with \\>230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.}", + issn = {0305-1048}, + doi = {10.1093/nar/gkac247}, + url = {https://doi.org/10.1093/nar/gkac247}, + eprint = {https://academic.oup.com/nar/article-pdf/50/W1/W345/45189566/gkac247.pdf}, +} + +@article{bioimageWorkflows, + title = {Bioimage analysis workflows: community resources to navigate through a complex ecosystem}, + volume = {10}, + ISSN = {2046-1402}, + url = {https://doi.org/10.12688/f1000research.52569.1}, + DOI = {10.12688/f1000research.52569.1}, + journal = {F1000Research}, + publisher = {F1000 Research Ltd}, + author = {Paul-Gilloteaux, Perrine and Tosi, Sébastien and Hériché, Jean-Karim and Gaignard, Alban and Ménager, Hervé and Marée, Raphaël and Baecker, Volker and Klemm, Anna and Kalaš, Matúš and Zhang, Chong and Miura, Kota and Colombelli, Julien}, + year = {2021}, + month = apr, + pages = {320} +} + +@article{black2021edam, + title={EDAM: The bioscientific data analysis ontology (update 2021)[version 1; not peer reviewed]}, + author={Black, Melissa and Lamothe, Lucie and {Hager Eldakroury} and Kierkegaard, Mads and {Ankita Priya} and Machinda, Anne and Khanduja, Uttam Singh and {Drashti Patoliya} and {Rashika Rathi} and {Tawah Peggy Che Nico} and Umutesi, Gloria and Blankenburg, Claudia and Op, Anita and Chieke, Precious and {Omodolapo Babatunde} and Laurie, Steve and Neumann, Steffen and Schw\"{a}mmle, Veit and Kuzmin, Ivan and Hunter, Chris and Karr, Jonathan and Ison, Jon and Gaignard, Alban and Brancotte, Bryan and Ménager, Hervé and {Matúš Kalaš}}, + year={2022}, + doi={10.7490/f1000research.1118900.1}, + journal={F1000Research}, + publisher={F1000} +} + +@article{batut_community-driven_2018, + title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}}, + volume = {6}, + issn = {24054712}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S2405471218302308}, + doi = {10.1016/j.cels.2018.05.012}, + language = {en}, + number = {6}, + urldate = {2024-02-26}, + journal = {Cell Systems}, + author = {Batut, Bérénice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Guéguen, Loraine and Čech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivière, Delphine and Le Corguillé, Gildas and Manke, Thomas and Mareuil, Fabien and Ramírez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Grüning, Björn}, + month = jun, + year = {2018}, + pages = {752--758.e1}, +} + +@article{Hiltemann_2023, + doi = {10.1371/journal.pcbi.1010752}, + url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752}, + year = 2023, + month = {jan}, + publisher = {Public Library of Science ({PLoS})}, + volume = {19}, + number = {1}, + pages = {e1010752}, + author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, + editor = {Francis Ouellette}, + title = {Galaxy Training: A powerful framework for teaching!}, + title = {{Galaxy Training: A powerful framework for teaching!}}, + journal = {PLoS Computational Biology} +} + + +@article{yuen_dockstore_2021, + title = {The {Dockstore}: enhancing a community platform for sharing reproducible and accessible computational protocols}, + volume = {49}, + issn = {0305-1048}, + shorttitle = {The {Dockstore}}, + url = {https://doi.org/10.1093/nar/gkab346}, + doi = {10.1093/nar/gkab346}, + abstract = {Dockstore (\url{https://dockstore.org/}) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute's GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.}, + number = {W1}, + urldate = {2023-10-20}, + journal = {Nucleic Acids Research}, + author = {Yuen, Denis and Cabansay, Louise and Duncan, Andrew and Luu, Gary and Hogue, Gregory and Overbeck, Charles and Perez, Natalie and Shands, Walt and Steinberg, David and Reid, Chaz and Olunwa, Nneka and Hansen, Richard and Sheets, Elizabeth and O’Farrell, Ash and Cullion, Kim and O’Connor, Brian D. and Paten, Benedict and Stein, Lincoln}, + month = jul, + year = {2021}, + pages = {W624--W632}, +} + +@article{noauthor_implementing_nodate, + title = {Implementing {FAIR} {Digital} {Objects} in the {EOSC}-{Life} {Workflow} {Collaboratory}}, + url = {https://zenodo.org/records/4605654}, + doi = {10.5281/zenodo.4605654}, + abstract = {The practice of performing computational processes using workflows has taken hold in the biosciences as the discipline becomes increasingly computational. The COVID-19 pandemic has spotlighted the importance of systematic and shared analysis of SARS-CoV-2 and its data processing pipelines. This is coupled with a drive in the community towards adopting FAIR practices (Findable, Accessible, Interoperable, and Reusable) not just for data, but also for workflows, and to improve the reproducibility of processes, both manual and computational. EOSC-Life brings together 13 of the Life Science ‘ESFRI’ research infrastructures to create an open, digital and collaborative space for biological and medical research. The project is developing a cloud-based workflow collaboratory to drive implementation of FAIR workflows across disciplines and RI boundaries, and foster tool-focused collaborations and reuse between communities via the sharing of data analysis workflows. The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows. As such it is an example of the Canonical Workflow Frameworks for Research (CWFR) vision in practice. EOSC-Life is made up of established research infrastructures ranging from biobanking and clinical trial management, through to coordinating biomedical imaging and plant phenotyping to multi-omic and systems-based data analysis. The heterogeneity of the disciplines is reflected in the diversity of their data analysis needs and practices and the variety of workflow management systems they use. Many have specialist platforms developed over years. Workflow management systems in common use include Galaxy, Snakemake, and Nextflow, and more specialist, domain-specific systems such as SCIPION. To serve the needs of this established and diverse community, EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. The registry adopts common practices, e.g.use of GitHub repositories, and supports integration with the ecosystem of tool packages, assisted by registries (bio.tools, biocontainers), and services for testing and benchmarking workflows (OpenEBench, LifeMonitor). As an umbrella registry, the Hub makes workflows Findable and Accessible by indexing workflows across workflow management systems and their native repositories, while providing rich standardized metadata. Interoperability and Reusability is supported by standardized descriptions of workflows and packaging of workflow components, developed in close collaboration with the communities. The WorkflowHub creates a place for registering and discovering libraries of workflows developed by collaborating teams, with suitable features for versioning, credit, analytics, and import/export needed to support the reuse of workflows, the development of sub-workflows as canonical steps and ultimately the identification of common patterns in the workflows. At the heart of the collaboratory is a Digital Object framework for documenting and exchanging workflows annotated with machine processable metadata produced and consumed by the participating platforms. The Digital Object framework is founded on several needs: Describing a workflow and its steps in a canonical, normalised and WfMS independent way: we use the Common Workflow Language (CWL), more specifically the Abstract CWL (non-executable) description variant to accompany the native workflow definitions. This presents the structure, composed tools and external interface in an interoperable way across workflow languages. WfMS can generate abstract CWL, already demonstrated for Galaxy, next to the ‘native’ Galaxy workflow description. This language duality is an important retention aspect of reproducibility, as the structure and metadata of the workflow can be accessed independent of its native format as CWL, even if that may no longer be executable, capturing the canonical workflow in a FAIR format. The co-presence of the native format enables direct reuse in the specific WfMS, benefitting from all its features. Metadata about a workflow and its tools using a minimal information model: we use the Bioschemas profiles Computational Tool, Computational Workflow and Formal Parameter which are discipline independent, opinionated conventions for using schema.org annotations. Bioschemas enables us to capture and publish workflow registrations and their metadata as FAIR Digital Objects. The EDAM Ontology is further used to add bioinformatics-specific metadata, such as strong typing of inputs and outputs, within both Abstract CWL and Bioschemas annotations. Organising and packaging the definitions and components of a workflow with their associated objects such as test data: we use a Workflow profile specialisation of RO-Crate, a community developed standardised approach for research output packaging with rich metadata. RO-Crate provides us the ability to package executable workflows, their components such as example and test data, abstract CWL, diagrams and their documentation. This makes workflows more readily re-usable. RO-Crate is the base unit of upload and download at the WorkflowHub. As CWFR Digital Objects of workflows, RO-Crates are activation-ready and circulated between the different services for execution and testing. Identifiers for all the components: like FAIR Digital Objects, RO-Crates can be metadata-rich bags of identifiers and can themselves be assigned permanent identifiers. This enables the full description of a computational analysis, from input data, over tools and workflows, to final results. Using these components we have built an environment that supports the Workflow Life Cycle, from abstract description, through to a specific rendering in a WfMS to its execution and the documentation of its run provenance, results and continued testing.}, + language = {en}, + urldate = {2023-10-20}, + author = {Goble, Carole and Soiland-Reyes, Stian and Bacall, Finn and Owen, Stuart and Williams, Alan and Eguinoa, Ignacio and Droesbeke, Bert and Leo, Simone and Pireddu, Luca and Rodríguez-Navas, Laura and Fernández, José and Capella-Gutierrez, Salvador and Ménager, Hervé and Grüning, Björn and Serrano-Solano, Beatriz and Ewels, Philip and Coppens, Frederik}, + year = {2021}, +} + +@article{callahan2016dada2, + title = {{DADA2}: High-resolution sample inference from {Illumina} amplicon data}, + author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, + journal = {Nature methods}, + volume = {13}, + number = {7}, + pages = {581--583}, + year = {2016}, + publisher = {Nature Publishing Group US New York}, + url = {https://doi.org/10.1038/nmeth.3869}, + doi = {10.1038/nmeth.3869}, +} + +@article{bolyen2019reproducible, + title={Reproducible, interactive, scalable and extensible microbiome data science using {QIIME 2}}, + author={Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and others}, + journal={Nature biotechnology}, + volume={37}, + number={8}, + pages={852--857}, + year={2019}, + publisher={Nature Publishing Group}, + url = {https://doi.org/10.1038/s41587-019-0209-9}, + doi = {10.1038/s41587-019-0209-9}, +} + +@misc{conda, + title = {Anaconda Software Distribution}, + url = {https://anaconda.com}, + urldate = {2016-11-01} +} + +@article{biotoolsSchema, + author = {Ison, Jon and Ienasescu, Hans and Rydza, Emil and Chmura, Piotr and Rapacki, Kristoffer and Gaignard, Alban and Schwämmle, Veit and van Helden, Jacques and Kala{\v{s}}, Mat{\'u}{\v{s}} and M{\'e}nager, Herv{\'e}}, + title = "{biotoolsSchema: a formalized schema for bioinformatics software description}", + journal = {GigaScience}, + volume = {10}, + number = {1}, + pages = {giaa157}, + year = {2021}, + month = {01}, + issn = {2047-217X}, + doi = {10.1093/gigascience/giaa157}, + url = {https://doi.org/10.1093/gigascience/giaa157}, + eprint = {https://academic.oup.com/gigascience/article-pdf/10/1/giaa157/36126150/giaa157.pdf}, +} + +@article{Ison2019, + title = {The bio.tools registry of software tools and data resources for the life sciences}, + volume = {20}, + ISSN = {1474-760X}, + url = {http://doi.org/10.1186/s13059-019-1772-6}, + DOI = {10.1186/s13059-019-1772-6}, + number = {1}, + journal = {Genome Biology}, + publisher = {Springer Science and Business Media LLC}, + author = {Ison, Jon and Ienasescu, Hans and Chmura, Piotr and Rydza, Emil and M{\'e}nager, Herv{\'e} and Kala{\v{s}}, Mat{\'u}{\v{s}} and Schw\"{a}mmle, Veit and Gr\"{u}ning, Bj\"{o}rn and Beard, Niall and Lopez, Rodrigo and Duvaud, Severine and Stockinger, Heinz and Persson, Bengt and Vařeková, Radka Svobodová and Raček, Tomáš and Vondrášek, Jiří and Peterson, Hedi and Salumets, Ahto and Jonassen, Inge and Hooft, Rob and Nyr\"{o}nen, Tommi and Valencia, Alfonso and Capella, Salvador and Gelpí, Josep and Zambelli, Federico and Savakis, Babis and Leskošek, Brane and Rapacki, Kristoffer and Blanchet, Christophe and Jimenez, Rafael and Oliveira, Arlindo and Vriend, Gert and Collin, Olivier and van Helden, Jacques and Løngreen, Peter and Brunak, Søren}, + year = {2019}, + month = aug +} + +@misc{zierep_galaxy_tool_metadata_extractor_2024, + title={How to increase the findability, visibility, and impact of Galaxy tools for your scientific community}, + url={osf.io/preprints/biohackrxiv/qjbxc}, + DOI={10.37044/osf.io/qjbxc}, + publisher={BioHackrXiv}, + author={Zierep, Paul and Batut, Bérénice and Kala{\v{s}}, Mat{\'u}{\v{s}} and Kayikcioglu, Tunc and Nasr, Engy and Soranzo, Nicola and Thang, Wai C and Wang, Joseph and Gustafsson, Ove J R}, + year={2024}, + month={Apr} +} \ No newline at end of file diff --git a/docs/publications/microgalaxy_annotation_hackathon/paper.md b/docs/publications/microgalaxy_annotation_hackathon/paper.md new file mode 100644 index 00000000..e7d91ef9 --- /dev/null +++ b/docs/publications/microgalaxy_annotation_hackathon/paper.md @@ -0,0 +1,280 @@ +--- +title: 'How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources' +title_short: 'Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources' +tags: + - annotation + - microbial + - Galaxy + - bio.tools + - EDAM + - microbiology + - microbiome + - workflows + - training +authors: + - name: Bérénice Batut + orcid: 0000-0001-9852-1987 + affiliation: 1, 2 + - name: Matthias Bernt + orcid: 0000-0003-3763-0797 + affiliation: 3 + - name: Mina Hojat Ansari + affiliation: 4 + - name: Matúš Kalaš + orcid: 0000-0002-1509-4981 + affiliation: 5 + - name: Paul Klemm + orcid: 0000-0002-3609-5713 + affiliation: 6 + - name: Romane Libouban + orcid: 0009-0001-4920-9951 + affiliation: 7 + - name: Engy Nasr + orcid: 0000-0001-9047-4215 + affiliation: 4 + - name: Claire Rioualen + affiliation: 1 + - name: Wai Cheng Thang + orchid: 0000-0002-1480-3563 + affiliation: 8, 9 + - name: Rand Zoabi + orcid: 0009-0000-2501-8053 + affiliation: 4 + - name: Paul Zierep + orcid: 0000-0003-2982-388X + affiliation: 4 +affiliations: + - name: Institut Français de Bioinformatique, CNRS UAR 3601, Évry, France + index: 1 + - name: Mésocentre Clermont-Auvergne, Université Clermont Auvergne, Aubiere, France + index: 2 + - name: Department Computational Biology & Chemistry, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany + index: 3 + - name: Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany + index: 4 + - name: Department of Informatics, University of Bergen, Norway; and ELIXIR Norway + index: 5 + - name: Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany + index: 6 + - name: GenOuest, University of Rennes, INRIA, CNRS, IRISA, Rennes, France + index: 7 + - name: Queensland Cyber Infrastructure Foundation (QCIF), Australia + index: 8 + - name: Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia + index: 9 +date: 29 March 2024 +bibliography: paper.bib +authors_short: Batut \emph{et al.} +group: BioHackrXiv +event: Other +biohackathon_name: Improving the annotation of Galaxy resources for microbial data resources +biohackathon_url: https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-annotation/ +biohackathon_location: Online +git_url: https://github.com/galaxyproject/galaxy_tool_metadata_extractor/tree/main/docs/publications/microgalaxy_annotation_hackathon +--- + +# Introduction + +Galaxy [@citesAsAuthority:10.1093/nar/gkac247] is a web-based data analysis platform initially developed for bioinformatics but that expanded its scope over the years to become a global and cross-domain community. + +Galaxy offers almost 10,000 different tools. To solve the visibility of tools across this ecosystem, a pipeline ([Galaxy Tool Metadata Extractor](https://github.com/galaxyproject/galaxy_tool_metadata_extractor)) [@citesAsAuthority:zierep_galaxy_tool_metadata_extractor_2024] was developed at the [ELIXIR BioHackathon Europe 2023](https://2023.biohackathon-europe.org) that collects Galaxy wrappers from a list of GitHub repositories and automatically extracts their metadata (including Conda version [@citesAsAuthority:conda], bio.tools identifier [@citesAsAuthority:biotoolsSchema, @usesDataFrom:Ison2019], BIII identifier [@citesAsAuthority:bioimageWorkflows], and EDAM ontology [@usesDataFrom:black2021edam], tool availability on public servers, usage statistics on the [Europen Galaxy Server](usegalaxy.eu)). The pipeline can filter its inputs to only include tools that are relevant to a specific research community. + +While developing this pipeline, we realized many tools miss proper annotations. Parallel to the pipeline development, annotation guidelines were established to solve this issue. An effort was started to update 50+ Galaxy tools, link them to their respective bio.tools entries, and collectively peer-review the results. However, that was far from enough to properly annotate all Galaxy tools and other types of Galaxy resources like training material and workflows. + +[microGalaxy](https://galaxyproject.org/community/sig/microbial/) is a community of practice within the Galaxy community that focuses on resources related to microbial research. Using Galaxy Tool Metadata Extractor, the microGalaxy community obtained a list of 260+ Galaxy tools related to microbial data analysis. Within this list, only half of them were linked to bio.tools entries, and many others had vague or very generic EDAM annotations in their bio.tools entries. The microGalaxy community decided to continue the work of improving the connection between Galaxy tools and bio.tools and improving the bio.tools entries. + +In addition to the tools, the microGalaxy community offers also other resources (30+ tutorials, 30+ workflows) that are also not properly annotated using ontologies like EDAM. Annotating all mentioned resources would improve their findability but also allow for aggregation and display of resources covering similar topics. + +To facilitate this work and work on a proof-of-concept for other communities, the microGalaxy community organized an online hackathon to improve the annotation of Galaxy resources and expand Galaxy Tool Metadata Extractor to other resources like tutorials and workflows. + +# Methods + +## Initial objectives + +The initial objectives of this hackathon were to improve the annotation of the Galaxy resources (tools, training, workflows) for microbial data analysis by: + +* Linking [microbial Galaxy tools](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/) to [bio.tools](http://bio.tools) to obtain [EDAM ontology](https://edamontology.org/page) annotation +* Improving bio.tools annotations +* Annotating [existing microbial-related tutorials](https://training.galaxyproject.org/training-material/search2?query=microgalaxy) with EDAM terms +* Reflecting on the addition of EDAM terms to workflows +* Reflecting on missing terms in the EDAM ontology for microbial data analyses +* Brainstorming on a way to connect tool annotations to improve training and workflow annotations + +## Organization + +The hackathon was held online from March 11th to 15th 2024. It was free of cost. A Zoom room was open the whole week from 9am to 5pm CET. The [microGalaxy Matrix chat](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im) was also used for communication. +Two daily stand-ups were done (one at 9:30 am CET and one at 4:00 pm CET) to accommodate different time zones. Additionally two brainstorming meetings on crucial subjects were planned. + +The hackathon was widely advertised by creating an event on the [Galaxy Hub website](https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-annotation/), the [IFB catalog](https://catalogue.france-bioinformatique.fr/event/604/) and [de.NBI website](https://www.denbi.de/training-courses-2024/1705-hackathon-improving-the-annotation-of-galaxy-resources-for-microbial-data-analysis-and-beyond), by sharing the information on different mailing lists and several community channels (Slacks or Matrix), and by spreading on social media. + +## Coordination + +The work during the week was coordinated using a [single Google document](https://docs.google.com/document/d/1B125dSKhB6AevnyShSi_zXIXUQd49tvNYfWHuyqmArY/edit?usp=sharing) that contained all information related to this hackathon (schedule, template for advertisement, pre-registration, etc). In this document, we also created a "How to contribute" section with step-by-step information on the different possible ways to contribute, in particular using the tutorial. + +In order to track the work and avoid work duplication, a ["tracking" spreadsheet](https://docs.google.com/spreadsheets/d/1EQMLJFKIt3ucSyt1aPAUQgGDfgbPFtKNTf7PhSe8pYQ/edit?usp=sharing) was created before the event. In this spreadsheet, several sheets were created and pre-filled: (i) "Galaxy Tools not linked to bio.tools id" with their metadata to track the bio.tools entry creation and the linking between bio.tools and the Galaxy tool, (ii) "Galaxy Tools linked to bio.tools id" to track bio.tools EDAM annotation updates, (iii) "Microbial-related Galaxy Tools" to review the curated list of microbial-related tools, (iv) "Microbial-related Tutorials" to track the EDAM topics identification and tutorial update. A last sheet was added to get an overview of the progress in the different sheets. + +This sheet along with the "How to contribute" section was introduced on the first day and to any newcomer during the week. + +The daily stand-up meetings were really useful for the coordination. In the 9:30 am CET meetings, participants from the APAC time zone shared their achievements for the day and participants from the EMEA time zone shared their objectives for the day. In the 4:00 pm CET meetings, participants from the EMEA time zone shared their achievements for the day. + +# Outcomes + +## Participants + +During the week, 15+ people from all over the world joined the effort, either just to discuss and learn about our efforts or more actively. It was a great opportunity to connect with members of other communities like QIIME2 or NFDI4Microbiota. + +The most active contributors (10 persons) were from Australia, Germany, France, and Norway. + +## Annotation of the microbial-related resources + +Improving the annotation of the Galaxy resources for microbial data analysis was the main objective of this hackathon. The outcomes are far beyond what we expected. + +### Linking Galaxy Tools to bio.tools entries + +Before this hackathon, 98 Galaxy tools (of the 200 microbial-related tools) were not linked to bio.tools, either because no bio.tools entry exists or because it was not provided in the Galaxy tool itself. + +During the hackathon, **41** tools have been added to bio.tools. + +Most of the Galaxy tools have been linked to their corresponding bio.tools entries with the actual status being: + +Status | Galaxy tools +--- | --- +Pull Request merged | 33 +Pull Request created, but not merged | 53 +Tools left | 12 + +The tools left are complicated cases where tools are deprecated or duplicated. + +For the other tools, we encountered several issues during the hackathon that delayed the merging of the Pull Request. First, a lot of tools were not following current [best practices for Galaxy Tool development](https://galaxy-iuc-standards.readthedocs.io/en/latest/) so the linting of the continuous integration was failing. Once that was solved, tests were also failing for a bunch of tools. Fixing linting and test errors slowed down the process of the tool annotation but improved the quality of Galaxy tools. Secondly, Galaxy tool sources are stored in GitHub repositories where none of the current contributors have maintainer rights. + +### Review of bio.tools entries + +For the Galaxy tools already linked to bio.tools, we started to review the EDAM annotations in the corresponding bio.tools entries. + +Status | bio.tools entries +--- | --- +Reviewed | 25 +Ongoing review | 14 +To review | 103 + +Over 140+ Galaxy tools linked to bio.tools entries, we managed to review 25 bio.tools entries. 14 are currently ongoing, especially because we are waiting to have edit access to the bio.tools entries. + +For most of the tools already or under review, their EDAM annotations have to be updated because they are too large or missing some functionalities. We then need to continue the work started here to be able to use these annotations for offering a comprehensive list of tools given EDAM Topics and Operations. + +### Microbial-related Galaxy Tools + +Galaxy Tool Metadata Extractor extracted 400+ that might be of interest for microbial data analysis. We did our first curation during the BioHackathon in November 2023. During this hackathon, some fresh pair of eyes started to review the curated list. + +Status | Microbial-related Galaxy tool +--- | --- +To keep | 180 +To exclude | 145 +To review | 420 + +We will need to continue this work but we might use information from workflows and tutorials to automatically identify the essential tools to keep in this list. + +### Microbial-related Tutorials + +On the Galaxy Training Network (GTN) Materials [@citesAsAuthority:batut_community-driven_2018, @citesAsAuthority:Hiltemann_2023], the microGalaxy community offers 30+ tutorials. These tutorials were not annotated with EDAM Topic or Operation. + +During the hackathon, 33 tutorials were matched with EDAM topics, that were added using Pull Requests to [GTN GitHub repository](https://github.com/galaxyproject/training-material/). A similar effort is ongoing to annotate the topics offered on the GTN website with corresponding EDAM Topics. + +For EDAM Operation in tutorials, another approach will be implemented. Each tutorial comes with a list of tools. This list will be compared to the information extracted by Galaxy Tool Metadata Extractor and EDAM Operations of the tools will be added to the EDAM Operation of the tutorials. + + +## Improvements to Galaxy Tool Metadata Extractor + +Feedback from the annotation process was used to improve the Galaxy Tool Metadata Extractor. + +### Improvement of the bio.tools id extraction + +No bio.tools IDs were extracted when there was unnecessary white space in the Galaxy tool XML. It was fixed in Galaxy Tool Metadata Extractor code ([Pull request #1](https://github.com/galaxyproject/galaxy_tool_metadata_extractor/pull/69), [Pull request #2](https://github.com/galaxyproject/galaxy_tool_metadata_extractor/pull/70)). In the Galaxy code itself, two new tool linting rules have been added: [one to check the validity of bio.tools annotation is Galaxy tools](https://github.com/galaxyproject/galaxy/pull/17655) and one [to check for leading and trailing spaces +in the text of leaf elements in Galaxy tool XML files](https://github.com/galaxyproject/galaxy/pull/17656). These caused problems in the metadata extractor. + +Some tool suites like SPAdes include multiple bio.tools references to individual tools. To track those cases [all bio.tools references for a tool are collected and stored in an additional column](https://github.com/galaxyproject/galaxy_tool_metadata_extractor/pull/72). + +### New GitHub repository sources + +To extract tool suites, the Galaxy Tool Metadata Extractor uses the GitHub repositories which are processed by the [planemo monitor](https://github.com/galaxyproject/planemo-monitor). So tools stored in other repositories were not extracted and available in the tool tables. A [configuration option](https://github.com/galaxyproject/galaxy_tool_metadata_extractor/pull/71) was added that allows to add additional repositories, such as the [QIIME2 repository](https://github.com/qiime2/galaxy-tools) [@citesAsAuthority:bolyen2019reproducible]. + +### Availability on all public servers + +Initially, tools within a suite were checked if they were installed on the largest Galaxy servers (usegalaxy.eu, usegalaxy.org, usegalaxy.org.au). The ratio of installed tools on these servers was given in the suite row with one column per server. + +The approach was slightly modified. The tools within a suite are now checked if installed on the list of [all public servers](https://galaxyproject.org/use/). If at least one of them is installed, the server is listed in the new column `All Server Availability`. + +For each [UseGalaxy](https://galaxyproject.org/usegalaxy/) server, a column is added with the number of tools within the suite that is installed on the corresponding server. + +### Usage statistics + +Usage statistics of the tools on UseGalaxy Europe are extracted to obtain the overall tool usage as well as how many users executed the tool in the last two years. However, for some tools, these usage statistics could not be extracted. + +This is due to incorrect matching between the name of the wrapper suite and the name of the tool on the server. [It has been fixed by matching the name of the individual tool IDs included in the suite with the tool ID on the server](https://github.com/galaxyproject/galaxy_tool_metadata_extractor/pull/78). This allowed us to extract the tool usage statistics for all tools that are indeed installed on UseGalaxy Europe. + +### Tracking of tool extraction + +To track the progress in the number of extracted tools and their annotation, a script was developed to collect the tables generated by Galaxy Tool Metadata Extractor from every GitHub commit, including the automatic commits that are created by the bot every week to update the results with the newest tools as well as any commit that was used to improve the code. + +The script generates a plot that shows the evolution of time of the number of Galaxy suites, Galaxy suites linked to bio.tools entries, Galaxy suites with usage statistics, Galaxy suites with associated conda package, and the number of the tools installed on the UseGalaxy servers. + +![Progress of the Galaxy Tool Metadata Extractor: Number of tool suits and associated metadata for different time points of the project.](microGalaxy_tool_metadata_progress.png) + +### Landing page and interactive table update + +The [landing page and interactive table](https://github.com/supernord/galaxy_tool_extractor/tree/supernord-landing-page) are also being updated to make use of the [ELIXIR Toolkit Theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme). That will give a nicer table and page while being sure that the table can still be embedded into other webpages. + +## Reflexion on EDAM terms for microbiome + +In the latest version of EDAM, new topics have been added, including Multiomics (topic_4021) and metabarcoding (topic_4038). But there are still some missing terms to represent what certain tools or training are doing and for what they are useful. + +During the hackathon, we had a dedicated meeting to reflect on the EDAM terms for microbiome research. We suggested that some operations could become topics: Genome annotation, Genome assembly (if merged with the Sequence assembly topic), Multilocus sequence typing / Molecular typing / Genotyping. + +We also reflected on a new Microbiome or Biome (or maybe both) topic that could encompass several subtopics: Metagenomics, Metabarcoding, Metatranscriptomics, Metaproteomics, etc. + +Regarding assembly, "Sequence assembly" exists as a topic and an operation, and "Genome assembly" is an operation. But there are no concepts to represent Metagenomics assembly. It could be added as a new operation or topic. + +Finally, we discussed binning. There is a "Read binning" operation mentioning contigs in its description. It could be renamed to "Binning" only to avoid confusion and include two suboperations: taxonomic binning and composition binning. + +## More microbial related work + +During the hackathon, contributions went also beyond resource annotation and Galaxy Tool Metadata Extractor. + +### DADA2 + +[A workflow for DADA2](https://github.com/galaxyproject/iwc/pull/14) [@citesAsAuthority:callahan2016dada2] has been finalized for [IWC](https://github.com/galaxyproject/iwc), a GitHub repository with Galaxy Workflows maintained by the Intergalactic Workflow Commission, and is now listed in two workflows registries: [Dockstore](https://dockstore.org/organizations/iwc)[@citesAsAuthority:yuen_dockstore_2021] and [WorkflowHub](https://workflowhub.eu/workflows/790)[@citesAsAuthority:noauthor_implementing_nodate]. + +A [discussion with the DADA2 community](https://github.com/benjjneb/dada2/issues/1911) has been initialized in how the [existing DADA2 tutorial for R](https://benjjneb.github.io/dada2/tutorial.html) may be reused as a tutorial in the Galaxy Training material. + +### BIOM + +A [tool](https://github.com/galaxyproject/tools-iuc/pull/5865) has been added to allow the import of BIOM files into phyloseq objects and [a bug in the BIOM format tools has been fixed](https://github.com/galaxyproject/tools-iuc/pull/5875). + +### QIIME2 + +A [Galaxy metadata setting problem (for an unrelated datatype)](https://github.com/galaxyproject/galaxy/pull/17674) has been fixed which made it impossible to upload QIIME2 reference data to Galaxy. + +[QIIME2 workflows](https://github.com/galaxyproject/iwc/pull/354) are being added to IWC so they can be listed on [WorkflowHub](https://workflowhub.eu/) and [Dockstore](https://dockstore.org/). + +A [new QIIME2 tutorial has been linked in the Galaxy Training Network](https://github.com/galaxyproject/training-material/pull/4804). +The training materials have also been discussed with the QIIME2 developers. +As soon as more QIIME2 tutorials are available for Galaxy, more links will be created in the GTN. + +Other points were discussed: how reference data can be integrated into the QIIME2 Galaxy tools, how data parameters can be better annotated in the QIIME2 Galaxy tools, and possibilities for parallelization in upcoming QIIME2 releases. + +For the improvement of the datatype usage, a script has been developed that extracts the hierarchy of the Galaxy datatypes and their EDAM data and format annotations which may help the QIIME2 developers to develop the mapping. + +### Restructuring of the Microbiome Training Topic + +The Microbiome Topic that stored all microbiome-related resources of the Galaxy Training Network has been [restructured](https://github.com/galaxyproject/training-material/pull/4814). A better structure was obtained by adding subtopics: Metabarcoding, Metagenomics, and Metatranscriptomics. + +# Conclusion and outlook + +The hackathon was successful with outcomes beyond the initial expectations. This was only possible as a community effort. + +Using the work done during this hackathon, we can aggregate microbial-related Galaxy tool suites using their EDAM Topics and Operation and give more visibility to the available tools for different analyses. This can be done analogously for training resources and hopefully later for workflows. The Galaxy Tool Metadata extractor could then go beyond Galaxy tools and generate metadata for communities as a series of tables with curated and annotated Galaxy resources (tools, training, and workflows). These tables could be used in the community pages to give more visibility to the amazing work they are doing and help users find the resources they need. + +# Acknowledgements + +The Institut Français de Bioinformatique (IFB) is funded by the Programme d'Investissements d'Avenir (PIA), grant Agence Nationale de la Recherche, number ANR-11-INBS-0013. + +# References diff --git a/docs/publications/readme.md b/docs/publications/readme.md new file mode 100644 index 00000000..01126c3b --- /dev/null +++ b/docs/publications/readme.md @@ -0,0 +1,6 @@ +# Publications + +## BioHackrXiv + +* The outcome of the BH2023 +* Should follow this guidelines: [Submission guidelines](https://guide.biohackrxiv.org/submission_guidelines.html) \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 34ad35e7..f3246526 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,4 +4,5 @@ pyyaml numpy Pillow matplotlib -wordcloud \ No newline at end of file +wordcloud +owlready2 \ No newline at end of file diff --git a/results/all_tools.tsv b/results/all_tools.tsv index 54ed1436..72db7767 100644 --- a/results/all_tools.tsv +++ b/results/all_tools.tsv @@ -1,1332 +1,1428 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 (0/1) (0/1) (0/1) -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 (0/2) (0/2) (0/2) -braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) -braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.6 (0/1) (1/1) (1/1) -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest 0.1.0 openjdk (0/1) (0/1) (0/1) -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python (0/1) (0/1) (0/1) -helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 (0/1) (0/1) (1/1) -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 (0/1) (0/1) (0/1) -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl (0/1) (0/1) (0/1) -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest 0.1.0 openjdk (0/1) (0/1) (0/1) -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest 2.0 (0/4) (0/4) (0/4) -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests (0/3) (0/3) (3/3) -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ 0.3.1 (0/1) (0/1) (1/1) -TreeBest treebest_best TreeBeST best To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) -apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ 1.0+galaxy1 apoc 1b16 (1/1) (0/1) (1/1) -blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) -ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ 0.0.2 EXPORT_DIR_PREFIX (0/1) (0/1) (0/1) -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) -gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python (0/1) (0/1) (1/1) -hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) -hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) -lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) -miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 (0/1) (0/1) (0/1) -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ 1.0 rDock 2013.1 (0/1) (0/1) (0/1) -replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ 0.1 python (0/1) (0/1) (1/1) -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 (0/1) (0/1) (0/1) -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ 1.0 smina 2017.11.9 (1/1) (0/1) (1/1) -t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl (0/1) (0/1) (0/1) -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml 0.2.0 pandas (0/1) (0/1) (0/1) -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml 5.1.0 gawk (1/1) (1/1) (1/1) -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml 0.1 (0/1) (0/1) (0/1) -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml 0.1 (0/1) (0/1) (0/1) -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat 0.2 (0/1) (0/1) (0/1) -cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk 0.20.0 csvtk 0.29.0 (0/20) (0/20) (0/20) -ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 (0/1) (0/1) (0/1) -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml 0.3.0 kaptive 2.0.6 (0/1) (0/1) (0/1) -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml 2.3 kat 2.4.2 (0/1) (0/1) (0/1) -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml 2.3 kat 2.4.2 (0/1) (0/1) (0/1) -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) -mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base (0/1) (0/1) (0/1) -pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist 0.1.2 python (0/1) (0/1) (0/1) -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml 0.1.6 r (0/1) (0/1) (0/1) -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml (0/1) (0/1) (0/1) -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml 1.1 spades 3.15.5 (0/1) (0/1) (0/1) -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 (0/1) (0/1) (0/1) -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer 1.2 python (0/1) (0/1) (0/1) -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) -sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml 1.1.1 sistr_cmd 1.1.1 (0/1) (1/1) (1/1) -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools 1.1.2+galaxy1 sed (0/1) (0/1) (0/1) -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml 1.0.1 spolpred (0/1) (0/1) (0/1) -srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) -staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics 1.48.0 r-snow 0.4_1 (1/2) (2/2) (2/2) -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ 1.0.1+galaxy0 r-batch 1.1_4 (0/1) (0/1) (0/1) -genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ genform r8 (0/1) (0/1) (1/1) -influx_si influx_si metabolic flux estimation based on [in]stationary labeling Up-to-date https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ 7.0.1 influx_si 7.0.1 (0/1) (0/1) (0/1) -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO 1.10.0 bioconductor-ipo 1.28.0 (0/2) (0/2) (0/2) -isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ 1.0.0 python (0/1) (0/1) (0/1) -mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics 3.1.0 r-lme4 (0/1) (0/1) (0/1) -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics 2.2.1 r-base (0/1) (0/1) (0/1) -nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation 3.0.0 r-batch 1.1_4 (0/1) (0/1) (1/1) -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics 2.0.0 r-batch 1.1_4 (0/1) (0/1) (0/1) -nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing r-batch 1.1_4 (0/2) (2/2) (2/2) -normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization 1.0.7 r-batch 1.1_4 (0/1) (1/1) (1/1) -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit 3.3.2 physiofit 3.3.2 (0/1) (0/1) (0/1) -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics 1.0.1 physiofit_data_manager 1.0.1 (0/1) (0/1) (0/1) -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ 3.12.0 bioconductor-xcms 4.0.0 (9/10) (9/10) (10/10) -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 (0/9) (0/9) (9/9) -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 (0/1) (0/1) (0/1) -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 (0/26) (0/26) (0/26) -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io To update https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.9 genoboo 0.4.12 (0/1) (0/1) (1/1) -jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python (0/1) (0/1) (0/1) -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 (0/22) (0/22) (0/22) -w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master 0.98.18 r-base (0/1) (1/1) (1/1) -w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master 0.98.19 r-base (0/1) (1/1) (1/1) -w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master 0.98.2 coreutils 8.25 (0/1) (1/1) (1/1) -2d_auto_threshold 6541.0 39.0 ip_threshold Automatic thresholding scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) -2d_feature_extraction 13760.0 19.0 ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ 0.1.1-2 pandas (0/1) (1/1) (1/1) -2d_filter_segmentation_by_features 6834.0 18.0 ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) -2d_histogram_equalization 656.0 39.0 ip_histogram_equalization 2d histogram equalization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_histogram_equalization imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) -2d_simple_filter 6156.0 35.0 ip_filter_standard 2d simple filter scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_simple_filter imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ 0.0.3-3 scikit-image (0/1) (1/1) (1/1) -3d_tensor_feature_dimension_reduction ip_3d_tensor_feature_dimension_reduction Dimensionality reduction for features (channels) of 3D tensor data using UMAP To update https://github.com/BMCV/galaxy-image-analysis Imaging 3d_tensor_feature_dimension_reduction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ 0.0.1 numpy (0/1) (0/1) (0/1) -anisotropic_diffusion 40.0 ip_anisotropic_diffusion Anisotropic image diffusion To update https://github.com/bmcv Imaging anisotropic_diffusion imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -bfconvert 1523.0 38.0 ip_convertimage Convert image To update https://github.com/bmcv Imaging, Convert Formats bfconvert imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ 6.7.0+galaxy2 bftools 6.7.0 (0/1) (1/1) (1/1) -binary2labelimage 1273.0 34.0 ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ 0.5 scikit-image (0/1) (1/1) (1/1) -binaryimage2points 29.0 ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ 0.1-2 numpy (0/1) (0/1) (1/1) -bioformats2raw 9.0 bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 (0/1) (0/1) (1/1) -color-deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ 0.8-2 scikit-image (0/1) (0/1) (1/1) -concat_channels 78.0 3.0 ip_concat_channels Concatenate images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -coordinates_of_roi 16546.0 8.0 ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ 0.0.4-2 scikit-image (0/1) (0/1) (1/1) -count_objects 272.0 25.0 ip_count_objects Count Objects galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) -curl_post 440.0 27.0 curl_post Send file via cURL POST To update https://github.com/bmcv Data Export, Web Services curl_post imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post 0.0.2 curl (0/1) (0/1) (1/1) -curve_fitting 12.0 1.0 ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ 0.0.3-2 numpy (0/1) (0/1) (1/1) -detection_viz 46.0 2.0 ip_detection_viz Detection Visualization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ 0.3-2 scikit-image (0/1) (0/1) (1/1) -image_info 621.0 41.0 ip_imageinfo Extracts image metadata To update https://github.com/bmcv Imaging image_info imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ 5.7.1 bftools 6.7.0 (0/1) (1/1) (1/1) -image_registration_affine 12.0 2.0 ip_image_registration Intensity-based Image Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ 0.0.3-2 scikit-image (0/1) (0/1) (1/1) -imagecoordinates_flipaxis 21825.0 7.0 imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1-2 pandas (0/1) (0/1) (1/1) -labelimage2points 36.0 ip_labelimage_to_points Label Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -landmark_registration 857.0 9.0 ip_landmark_registration Landmark Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ 0.1.0-2 scikit-image (1/1) (0/1) (1/1) -mahotas-features ip_mahotas_features Compute image features using mahotas. To update https://github.com/luispedro/mahotas Imaging mahotas_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ 0.7-2 mahotas (0/1) (0/1) (1/1) -mergeneighboursinlabelimage 25.0 ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage 0.3-2 scikit-image (0/1) (0/1) (1/1) -overlay_images 60.0 21.0 ip_overlay_images Overlay two images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ 0.0.4 scikit-image (0/1) (0/1) (1/1) -permutate_axis 42.0 ip_permutate_axis Permutates axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -points2binaryimage 41.0 2.0 ip_points_to_binaryimage Points to Binary Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ 0.2-1 scikit-image (0/1) (0/1) (1/1) -points2labelimage 66.0 ip_points_to_label Points to label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ 0.3-2 numpy (0/1) (0/1) (1/1) -points_association_nn 29.0 2.0 ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ 0.0.3-2 numpy (0/1) (0/1) (1/1) -projective_transformation 44.0 1.0 ip_projective_transformation Projective transformation galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 0.1.2-2 scikit-image (0/1) (0/1) (1/1) -projective_transformation_points 21208.0 9.0 ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ 0.1.1-2 scikit-image (0/1) (0/1) (1/1) -rfove 7.0 rfove Perform segmentation region-based fitting of overlapping ellipses rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ 2023.11.12 (0/1) (0/1) (1/1) -scale_image 615.0 9.0 ip_scale_image Scale image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ 0.4-2 pillow (0/1) (0/1) (1/1) -segmetrics 3.0 2.0 ip_segmetrics Image segmentation and object detection performance measures segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis Up-to-date https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ 1.4 segmetrics 1.4 (0/1) (0/1) (1/1) -slice_image 102.0 ip_slice_image Slice image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3-2 scikit-image (0/1) (0/1) (1/1) -split_labelmap 42.0 ip_split_labelmap Split Labelmaps galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -spot_detection_2d 16.0 3.0 ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ 0.0.3-2 imageio (0/1) (0/1) (1/1) -superdsm 16.0 2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.1.3 (0/1) (0/1) (1/1) -unzip 5370.0 508.0 unzip Unzip file To update https://github.com/bmcv Convert Formats unzip imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ 6.0 unzip (0/1) (1/1) (1/1) -visceral-evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 (0/1) (0/1) (1/1) -wsi_extract_top_view 38.0 ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -add_value 33763.0 356.0 addValue Add a value as a new column. To update Text Manipulation add_value devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value 1.0.1 perl (1/1) (1/1) (1/1) -annotation_profiler 2.0 Annotation_Profiler_0 Profile Annotations for a set of genomic intervals To update Genomic Interval Operations annotation_profiler devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler 1.0.0 bx-python 0.10.0 (1/1) (0/1) (1/1) -best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) -bowtie_wrappers 22988.0 506.0 bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 (0/1) (1/1) (1/1) -canonical_correlation_analysis 72.0 10.0 cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis 1.0.0 R (0/1) (0/1) (1/1) -categorize_elements_satisfying_criteria 40.0 1.0 categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria 1.0.0 (0/1) (1/1) (1/1) -ccat 165.0 15.0 peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat 0.0.2 ccat 3.0 (0/1) (0/1) (1/1) -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) -change_case ChangeCase Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case 1.0.1 perl (1/1) (1/1) (1/1) -compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) -compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) -compute_q_values 35.0 compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values 1.0.1 R (0/1) (0/1) (0/1) -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters 1.0.0 (1/1) (1/1) (0/1) -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters 1.0.1 python (1/1) (1/1) (1/1) -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc 1.0.0 (0/1) (0/1) (0/1) -correlation 809.0 47.0 cor2 Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation 1.0.0 rpy (0/1) (1/1) (1/1) -count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) -ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) -cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) -cummerbund_to_tabular 1204.0 13.0 cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular 1.0.1 (1/1) (0/1) (1/1) -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns 1.0.2 (1/1) (1/1) (1/1) -delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) -dgidb_annotator 231.0 30.0 dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator 0.1 (0/1) (0/1) (1/1) -divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) -draw_stacked_barplots 173.0 12.0 draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots 1.0.0 R (0/1) (1/1) (1/1) -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_var_perfeature 36.0 dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature 1.0.2 r-bitops (1/1) (1/1) (1/1) -express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) -fasta_compute_length 7758.0 380.0 fasta_compute_length Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.3 python (1/1) (1/1) (1/1) -fasta_concatenate_by_species 35793.0 88.0 fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -fasta_filter_by_length 48649.0 350.0 fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length 1.2 python (1/1) (1/1) (1/1) -fasta_to_tabular 105841.0 622.0 fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular 1.1.1 python (1/1) (1/1) (1/1) -fastq_trimmer_by_quality 5485.0 459.0 fastq_quality_trimmer FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual 1.0.0 (0/1) (0/1) (0/1) -featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter 2.0.0 bx-python 0.10.0 (1/1) (0/1) (1/1) -filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) -generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) -gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) -hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) -histogram 2367.0 94.0 histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 1.0.4 rpy2 2.7.8 (1/1) (1/1) (1/1) -indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) -kernel_canonical_correlation_analysis 69.0 2.0 kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis 1.0.0 rpy (1/1) (0/1) (1/1) -kernel_principal_component_analysis 155.0 13.0 kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis 1.0.0 rpy (1/1) (0/1) (1/1) -lastz_paired_reads 9.0 1.0 lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 (0/1) (1/1) (1/1) -lda_analysis 148.0 18.0 lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis 1.0.1 R (1/1) (0/1) (1/1) -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression 1.0.1 R (1/1) (0/1) (0/1) -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) -megablast_xml_parser 338.0 36.0 megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser 1.0.1 python (1/1) (0/1) (1/1) -merge_cols 21906.0 536.0 mergeCols1 Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols 1.0.3 python (1/1) (1/1) (1/1) -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability 1.1.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -mine 11.0 2.0 maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine 0.0.1 MINE (1/1) (0/1) (1/1) -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) -mutate_snp_codon 47.0 mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon 1.0.0 (1/1) (0/1) (1/1) -partialr_square partialRsq Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square 1.0.0 R (1/1) (0/1) (0/1) -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation 1.0.0 (0/1) (0/1) (0/1) -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp 1.0.0 (0/1) (0/1) (0/1) -pileup_interval 632.0 15.0 pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval 1.0.3 bx-python 0.10.0 (1/1) (1/1) (1/1) -pileup_parser 3158.0 169.0 pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser 1.0.2 perl (1/1) (1/1) (1/1) -plot_from_lda 73.0 9.0 plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda 1.0.1 R (1/1) (0/1) (1/1) -principal_component_analysis 9986.0 88.0 pca1 Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis 1.0.2 rpy (1/1) (0/1) (1/1) -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 1.0.1 bx-python 0.10.0 (0/1) (0/1) (0/1) -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning 1.0.0 (1/1) (1/1) (1/1) -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) -sam2interval 1189.0 20.0 sam2interval Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval 1.0.2 python (1/1) (1/1) (1/1) -sam_bitwise_flag_filter 261.0 1.0 sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter 1.0.1 python (1/1) (1/1) (0/1) -scatterplot 1637.0 61.0 scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot 1.0.3 numpy (1/1) (0/1) (1/1) -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) -short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) -short_reads_trim_seq 220.0 21.0 trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq 1.0.0 (1/1) (0/1) (1/1) -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning 1.0.0 (1/1) (1/1) (1/1) -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail 1.0.0 (1/1) (1/1) (1/1) -sicer 374.0 5.0 peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer 1.1 SICER 1.1 (1/1) (1/1) (1/1) -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads 1.0.0 (0/1) (0/1) (0/1) -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) -t_test_two_samples 210.0 6.0 t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples 1.0.1 R (1/1) (1/1) (1/1) -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar 0.2 annovar (0/1) (0/1) (0/1) -tabular_to_fasta 319234.0 601.0 tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta 1.1.1 python (1/1) (1/1) (1/1) -tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat 1.5.0 samtools 1.19.2 (0/1) (0/1) (0/1) -tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 2.1.1 bowtie2 2.5.3 (1/1) (1/1) (1/1) -tophat_fusion_post 216.0 15.0 tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post 0.1 blast+ (0/1) (1/1) (1/1) -trimmer 6058.0 188.0 trimmer Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer 0.0.1 (1/1) (1/1) (1/1) -ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) -varscan_version_2 5191.0 246.0 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 2.4.2 varscan 2.4.6 (1/1) (1/1) (1/1) -vcf2pgsnp 206.0 15.0 vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp 1.0.0 (1/1) (0/1) (1/1) -vcf_annotate 1.0 vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate 1.0.0 (0/1) (0/1) (0/1) -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract 1.0.0 (0/1) (0/1) (0/1) -vcf_filter 388.0 63.0 vcf_filter Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter 1.0.0 (0/1) (0/1) (1/1) -vcf_intersect 19.0 vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect 1.0.0 (0/1) (0/1) (0/1) -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) -xy_plot 5890.0 344.0 XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot 1.0.2 r-base (1/1) (1/1) (1/1) -basecoverage 307.0 2.0 gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -cluster 791.0 1.0 gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -complement 233.0 1.0 gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -concat 564897.0 309.0 gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat 1.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -coverage 1489.0 17.0 gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -flanking_features 671.0 20.0 flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features 4.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -get_flanks 324380.0 555.0 get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -intersect 347919.0 1003.0 gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -join 329478.0 284.0 gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -merge 563676.0 193.0 gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -subtract 564149.0 182.0 gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -subtract_query 1014.0 55.0 subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query 0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -tables_arithmetic_operations 2207.0 14.0 tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl (0/1) (0/1) (1/1) -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) -snpfreq 37.0 7.0 hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq 1.0.1 R (1/1) (1/1) (1/1) -find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) -kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk (1/1) (1/1) (1/1) -lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) -poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 (0/1) (1/1) (1/1) -t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -vcftools_annotate 171.0 24.0 vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate 0.1 echo (1/1) (0/1) (1/1) -vcftools_compare 531.0 34.0 vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 (0/1) (0/1) (1/1) -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.19.2 (0/1) (0/1) (0/1) -vcftools_isec 498.0 35.0 vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 (0/1) (1/1) (1/1) -vcftools_merge 953.0 68.0 vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 (0/1) (1/1) (1/1) -vcftools_slice 411.0 24.0 vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice 0.1 echo (1/1) (0/1) (1/1) -vcftools_subset 137.0 17.0 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) -10x_bamtofastq 228.0 46.0 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -agat 481.0 42.0 agat GTF/GFF analysis toolkit agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics Up-to-date https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.2.0 (0/1) (0/1) (1/1) -antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 (1/1) (1/1) (1/1) -atactk_trim_adapters 257.0 26.0 atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters 0.1.6 atactk 0.1.9 (0/1) (0/1) (1/1) -augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) -bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.0 (0/1) (0/1) (0/1) -bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools (0/1) (0/1) (1/1) -biomodelsML biomodels_biomd0000001066, biomodels_BIOMD0000001076 Random Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts To update https://www.ebi.ac.uk/biomodels/BIOMD0000001066 Machine Learning biomodels_biomd0000001066 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1 (0/2) (0/2) (1/2) -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) -bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (0/4) (4/4) -blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) -blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) -canu 13021.0 533.0 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 (0/1) (1/1) (1/1) -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools (0/23) (23/23) (23/23) -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.6 (0/1) (0/1) (1/1) -chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) -circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann Combine Metaphlan and HUMAnN """This tool combine MetaPhlAn outputs and HUMANnN outputs."" - Galaxy tool wrapper" Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 0.3.0 python (0/1) (0/1) (1/1) -compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs Compare HUMAnN2 outputs """This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples."" - Galaxy tool wrapper" Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) -cpat 134.0 21.0 cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.4 cpat 3.0.4 (1/1) (1/1) (1/1) -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) -diff 235.0 30.0 diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils (0/1) (0/1) (1/1) -diffbind 6264.0 250.0 Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind (0/1) (0/1) (0/1) -edta 484.0 58.0 edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta edta 2.2.0 (0/1) (0/1) (1/1) -epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 (0/1) (0/1) (1/1) -fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) -find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening 0.3 biopython 1.70 (1/1) (0/1) (1/1) -flye 20904.0 1499.0 flye Assembly of long and error-prone reads. To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.1 flye 2.9.3 (1/1) (1/1) (1/1) -footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) -format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ 1.0.0+galaxy1 (0/1) (0/1) (1/1) -format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output Format metaphlan2 output """This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)."" - Galaxy tool wrapper" Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 (0/1) (0/1) (1/1) -gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) -gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 (0/1) (0/1) (0/1) -graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 0.99 hclust2 1.0.0 (0/1) (0/1) (0/1) -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 (7/7) (0/7) (7/7) -hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler Up-to-date https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.8 (1/1) (1/1) (1/1) -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools 0.1.0 wget (0/1) (0/1) (1/1) -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.40 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) -instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) -itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 (0/1) (0/1) (0/1) -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) -lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data To update Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/mourisl/Lighter 1.0 lighter 1.1.2 (0/1) (0/1) (1/1) -mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.508 mafft 7.520 (2/2) (2/2) (2/2) -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ 0.9 (0/1) (0/1) (1/1) -mcl 29.0 10.0 mcl_clustering Markov Cluster Algorithm To update http://micans.org/mcl/ Sequence Analysis, Metagenomics mcl bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mcl 14.137 mcl 22.282 (0/1) (0/1) (0/1) -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 (0/1) (0/1) (0/1) -metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) -minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) -minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) -mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (0/1) (1/1) -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) -music_deconvolution 530.0 67.0 music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ 0.1.1 music-deconvolution 0.1.1 (5/5) (5/5) (4/5) -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 (0/4) (4/4) (4/4) -netboxr 11.0 5.0 netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening 1.6.0 bioconductor-netboxr 1.9.0 (0/1) (0/1) (1/1) -nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) -nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) -numeric_clustering 486.0 numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda (0/1) (0/1) (0/1) -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (0/140) (34/140) (135/140) -pandas_rolling_window 269.0 7.0 pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy (1/1) (0/1) (1/1) -peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf (0/1) (0/1) (0/1) -pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools postgresql (0/3) (0/3) (0/3) -pharmcat 82.0 14.0 pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat (1/1) (0/1) (1/1) -piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) -plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas (1/1) (1/1) (1/1) -plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) -plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) -protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) -protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) -racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads Genome assembly, Mapping assembly, Sequence trimming Whole genome sequencing, Sequence assembly, Plant biology Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) -repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn 0.2 (1/1) (1/1) (1/1) -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 (0/1) (0/1) (0/1) -antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) -aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) -blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) -cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy0 perl (0/1) (0/1) (1/1) -cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) -cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) -compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ 1.0 compalignp 1.0 (0/1) (0/1) (1/1) -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) -dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) -dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 (0/1) (0/1) (1/1) -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 (0/1) (0/1) (0/1) -dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) -infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs Up-to-date http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal 1.1.4 infernal 1.1.4 (0/6) (6/6) (6/6) -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) -intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) -kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) -mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) -mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 (0/1) (0/1) (1/1) -nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) -paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) -pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) -rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) -rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (0/1) -remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) -ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) -rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) -rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) -rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) -rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) -rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) -rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) -selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) -sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) -sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) -targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) -trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) -vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) -sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) -salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.2 (2/3) (1/3) (3/3) -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_slice, sambamba_sort, sambamba_view, sambamba_depth SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba sambamba 1.0 (0/7) (0/7) (0/7) -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed (0/1) (0/1) (0/1) -segemehl 1276.0 30.0 segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 (0/1) (0/1) (1/1) -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 (30/33) (14/33) (31/33) -splitfasta 1295.0 96.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 (1/1) (0/1) (1/1) -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy (0/1) (0/1) (1/1) -stress_ng 47.0 stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng 0.12.04 stress-ng (0/1) (0/1) (0/1) -add_line_to_file 14480.0 193.0 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) -column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 (1/1) (1/1) (1/1) -join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1) -split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1) -split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.1 python (1/1) (1/1) (1/1) -text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 0.1.1 coreutils 8.25 (19/19) (19/19) (19/19) -tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1) -trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) -uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.4 requests (1/1) (1/1) (1/1) -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) -wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) -align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.19.2 (0/2) (0/2) (0/2) -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.19.2 (0/1) (0/1) (0/1) -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.19.2 (0/1) (0/1) (0/1) -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.20 effectiveT3 1.0.1 (0/1) (0/1) (0/1) -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) -mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) -sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.19.2 (0/1) (0/1) (0/1) -samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.19.2 (1/1) (0/1) (1/1) -samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.19.2 (1/1) (1/1) (1/1) -seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) -seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) -seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) -venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) -abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr 1.0.14 abritamr 1.0.14 (0/1) (0/1) (0/1) -abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly To update http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss 2.3.6 abyss 2.3.7 (0/1) (1/1) (1/1) -adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) -add_input_name_as_column 83150.0 91.0 addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python (1/1) (0/1) (1/1) -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) -aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) -allegro allegro Linkage and haplotype analysis from deCODE allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ @VER@.0 allegro 3 (0/1) (0/1) (0/1) -amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 2.7.22 (0/19) (0/19) (19/19) -amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.11.26 (0/1) (0/1) (1/1) -ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.10.3 anndata 0.6.22.post1 (5/5) (3/5) (5/5) -annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.17.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) -arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (0/3) -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) -augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) -bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.9.2 (0/1) (1/1) (1/1) -bam_to_scidx 128.0 4.0 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx 1.0.1 openjdk (1/1) (0/1) (1/1) -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) -bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 (0/1) (0/1) (0/1) -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 (4/4) (0/4) (4/4) -barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) -basil 266.0 35.0 basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc 1.2.0 anise_basil 1.2.0 (1/1) (0/1) (1/1) -bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) -bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.01 bbmap 39.01 (1/6) (1/6) (5/6) -bcftools 524.0 78.0 bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools 1.15.1 bcftools 1.19 (0/5) (0/5) (0/5) -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). GA4GH Beacon Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 (0/3) (0/3) (3/3) -beagle 54.0 10.0 beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e (0/1) (0/1) (1/1) -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/ 2.4.41 bedops 2.4.41 (1/1) (0/1) (1/1) -bedtools 936832.0 6318.0 bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics To update https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 2.30.0 bedtools 2.31.1 (37/37) (37/37) (37/37) -bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka 0.2.3 berokka 0.2.3 (0/1) (1/1) (0/1) -binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! To update https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ 0.20.4 python-bioext 0.21.2 (2/2) (0/2) (2/2) -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python (1/1) (0/1) (1/1) -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) -biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast 1.7.0 magicblast 1.7.0 (0/1) (0/1) (1/1) -blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) -bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 2.5.0 bowtie2 2.5.3 (1/1) (1/1) (1/1) -bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken 2.9 bracken 2.9 (0/1) (0/1) (1/1) -breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc 0.35.5 breseq 0.38.2 (0/1) (1/1) (1/1) -busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.6.1 (1/1) (1/1) (1/1) -bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa 0.7.17 bwa 0.7.17 (2/2) (2/2) (2/2) -bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) -bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) -calculate_numeric_param 1393.0 8.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param 0.1.0 (0/1) (0/1) (1/1) -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) -cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) -cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) -charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt (0/1) (0/1) (0/1) -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) -chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 1.0.7 chopin2 (1/1) (0/1) (0/1) -chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) -circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) -circos 21787.0 1018.0 circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos 0.69.8 circos 0.69.9 (11/11) (11/11) (11/11) -cite_seq_count 18.0 1.0 cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.4 (1/1) (0/1) (1/1) -clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 0.1.12 clair3 1.0.5 (0/1) (0/1) (1/1) -clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins " - clustal2 - " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit 0.9.10 cnvkit 0.9.10 (0/17) (0/17) (17/17) -codeml 60901.0 29.0 codeml Detects positive selection To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) -collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) -collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) -column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.0 python (1/1) (1/1) (1/1) -column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) -column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python (1/1) (1/1) (1/1) -compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) -compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) -concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics To update https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm 0.6.1 coverm 0.7.0 (0/2) (0/2) (2/2) -crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) -crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) -cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt 4.6 cutadapt 4.6 (1/1) (1/1) (1/1) -cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv 1.0.8 cutesv 2.1.0 (0/1) (1/1) (1/1) -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) -das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics To update https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool 1.1.6 das_tool 1.1.7 (0/2) (0/2) (2/2) -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga 1.0.0 python (0/1) (0/1) (0/1) -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash 1.8 datamash 1.1.0 (3/3) (3/3) (3/3) -decontaminator 99.0 15.0 decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator 1.0.0 numpy (0/1) (0/1) (1/1) -deepmicro 501.0 3.0 deepmicro Representation learning and classification framework " - DeepMicro - " Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 (0/1) (0/1) (1/1) -deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) -deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) -deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) -deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis Transcriptomics To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) -dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) -diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond 2.0.15 diamond 2.1.8 (3/3) (3/3) (3/3) -diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. To update https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet 0.1.4 dimet 0.2.1 (0/1) (0/1) (0/1) -disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ disco 1.2 (1/1) (0/1) (1/1) -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.4.5 (0/2) (0/2) (2/2) -dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) -ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) -edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) -egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) -emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) -ena_upload 208.0 14.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload 0.6.3 ena-upload-cli 0.7.0 (0/1) (1/1) (1/1) -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch enasearch 0.2.2 (0/5) (0/5) (5/5) -ensembl_vep 2653.0 119.0 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep 110.1 ensembl-vep 111.0 (0/1) (0/1) (1/1) -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ 0.3.2 episcanpy 0.4.0 (2/3) (0/3) (3/3) -exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) -exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) -export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) -extract_genomic_dna 11348.0 285.0 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.10.0 (1/1) (0/1) (1/1) -fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) -fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) -fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy (1/1) (1/1) (1/1) -fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc 1.3 fastani 1.34 (0/1) (0/1) (1/1) -fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files " - fastp - " To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1) -fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc 0.74+galaxy0 fastqc 0.12.1 (1/1) (1/1) (1/1) -fastqe 4333.0 1266.0 fastqe FASTQE To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) -fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) -featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation Sequencing To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) -feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) -fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) -filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality " - filtlong - " Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) -flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) -fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ fraggenescan 1.31 (0/1) (1/1) (1/1) -freebayes 153548.0 3059.0 freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes 1.3.6 freebayes 1.3.7 (2/2) (2/2) (2/2) -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec 11.6 gawk (0/1) (0/1) (1/1) -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.8 (2/4) (0/4) (4/4) -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd 1.0.2 matplotlib (4/4) (0/4) (0/4) -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " - funannotate - " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 4.1.7.0 gatk4 4.4.0.0 (1/1) (0/1) (1/1) -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy 1.0.0 python (1/1) (0/1) (1/1) -gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) -gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) -genebed_maf_to_fasta 2.0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 (1/1) (1/1) (1/1) -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ 3.0.0 ghm 3.1 (0/1) (0/1) (0/1) -geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack numpy (1/1) (0/1) (0/1) -genomescope 2118.0 329.0 genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope 2.0 genomescope2 2.0 (1/1) (1/1) (1/1) -genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) -genrich 3515.0 79.0 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich 0.5+galaxy2 genrich 0.6.1 (1/1) (1/1) (1/1) -get_hrun 4.0 1.0 get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.1 (0/1) (0/1) (1/1) -getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle 1.7.7.0 getorganelle 1.7.7.0 (0/2) (2/2) (2/2) -gfa_to_fa 8274.0 332.0 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa 0.1.2 (1/1) (1/1) (1/1) -gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) -gffcompare 3477.0 381.0 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare 0.12.6 gffcompare 0.12.6 (1/1) (1/1) (1/1) -gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base (5/5) (2/5) (5/5) -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset 1.0 r-ggupset (0/1) (0/1) (0/1) -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) -goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) -goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ @TOOL_VERSION@+galaxy11 r-gprofiler2 (5/5) (0/5) (5/5) -graphembed 63.0 2.0 graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ 2.4 graph_embed 2.4 (1/1) (0/1) (1/1) -graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees To update https://bitbucket.org/nsegata/graphlan/overview Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ graphlan 1.1.3 (2/2) (2/2) (2/2) -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 357 ucsc-gtftogenepred 447 (1/1) (1/1) (1/1) -gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.1 (1/1) (1/1) (1/1) -gvcftools gvcftools_extract_variants To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools 0.1 gvcftools 0.17.0 (0/1) (0/1) (0/1) -gwastools gwastools_manhattan_plot gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 (0/2) (0/2) (2/2) -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) -hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog 1.3.6 hapog 1.3.7 (0/1) (0/1) (1/1) -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 3.1.3 r-gplots 2.17.0 (1/1) (1/1) (1/1) -heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. bionet BioNet This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) -hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff 3.1.5 hicstuff 3.2.1 (0/1) (0/1) (0/1) -hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) -hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ 1.3.1 python-hivclustering 1.6.8 (0/1) (0/1) (0/1) -hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families To update http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 3.3.2 hmmer 3.4 (0/12) (12/12) (12/12) -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) -htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis To update https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count 0.9.1+galaxy1 htseq 2.0.5 (1/1) (1/1) (1/1) -humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (6/13) (13/13) -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper 2.1.6 hybpiper 2.1.6 (0/1) (1/1) (0/1) -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ 2.5.47 hyphy 2.5.59 (17/17) (2/17) (17/17) -hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.1 icescreen 1.3.1 (0/1) (0/1) (0/1) -idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) -idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download 0.44.1 omero-py 5.11.1 (0/1) (0/1) (1/1) -iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain 1.5.3 instrain 1.8.0 (0/2) (0/2) (2/2) -integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis To update https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder 2.0.2 hmmer 3.4 (0/1) (1/1) (1/1) -intermine_galaxy_exchange 44.0 1.0 galaxy_intermine_exchange InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 (1/1) (1/1) (1/1) -interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) -interval2maf 14.0 3.0 Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.10.0 (1/1) (1/1) (1/1) -intervene 1497.0 136.0 intervene_pairwise, intervene_upset Create pairwise and upset plots intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene 0.6.5 intervene 0.6.5 (2/2) (0/2) (2/2) -iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood To update http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ 2.1.2 iqtree 2.2.6 (1/1) (1/1) (1/1) -irissv 29.0 4.0 irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ 1.0.4 samtools 1.19.2 (0/1) (0/1) (1/1) -isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) -isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 (3/3) (3/3) (3/3) -jasminesv 30.0 3.0 jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ 1.0.11 jasminesv 1.1.5 (1/1) (0/1) (1/1) -jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) -jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) -jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.0 (0/1) (1/1) (1/1) -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 (0/1) (0/1) (0/1) -jq 2312.0 21.0 jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq 1.0 jq 1.5 (1/1) (1/1) (1/1) -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 (1/1) (0/1) (1/1) -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ 0.48.0 kallisto 0.50.1 (2/2) (2/2) (2/2) -kc-align kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) -king 5.0 3.0 king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ 2.2.7 king 2.2.7 (0/1) (0/1) (1/1) -kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma 1.2.21 kma 1.4.9 (0/1) (0/1) (1/1) -kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) -kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) -kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (0/1) (1/1) -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 (1/6) (2/6) (6/6) -krocus krocus Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (0/1) -last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last 1205 last 1526 (0/5) (0/5) (5/5) -lastz 83331.0 188.0 lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz 1.04.22 lastz 1.04.22 (2/2) (2/2) (2/2) -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie 1.0.2 lcr_genie (0/1) (0/1) (0/1) -legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) -length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) -limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics To update http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom 3.50.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) -lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot 1.4.0 r-base (0/1) (0/1) (1/1) -links 405.0 77.0 links Scaffold genome assemblies with long reads. links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq 2.1.5 lofreq 2.1.5 (5/5) (5/5) (5/5) -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) -lumpy_sv 358.0 50.0 lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv 0.3.1 lumpy-sv 0.3.1 (0/2) (0/2) (2/2) -m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) -maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 0.99.12 maaslin2 0.99.12 (0/1) (0/1) (1/1) -macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) -maf_stats 8.0 2.0 maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 (1/1) (1/1) (1/1) -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck 0.5.9.2 mageck 0.5.9.5 (3/5) (5/5) (5/5) -maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt 0.5.3 malt 0.61 (0/1) (0/1) (1/1) -map_param_value 1528.0 9.0 map_param_value Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value 0.2.0 (1/1) (0/1) (1/1) -mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) -mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) -masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) -maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ maxbin2 2.2.7 (1/1) (1/1) (1/1) -mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) -megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) -megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.24.20 (0/7) (0/7) (7/7) -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_fimo meme_fimo A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. Sequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculation Sequence analysis, Genetic variation, Statistics and probability, Data mining To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) -meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) -merlin merlin Pedigree Analysis package merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) -merqury 2483.0 244.0 merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury 1.3 merqury 1.3 (1/1) (1/1) (1/1) -meryl 6785.0 350.0 meryl Meryl a k-mer counter. meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) -metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ 2.15 metabat2 2.15 (1/2) (1/2) (2/2) -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) -metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ 4.0.6 metaphlan 4.0.6 (1/4) (2/4) (4/4) -migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) -minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) -miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) -minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 2.26 minimap2 2.26 (1/1) (1/1) (1/1) -miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot 0.12 miniprot 0.12 (0/2) (0/2) (2/2) -mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 (0/1) (0/1) (1/1) -mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) -mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos 1.1.5 mitos 2.1.7 (1/2) (1/2) (2/2) -mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Taxonomic classification Immunoproteins, genes and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) -moabs 317.0 19.0 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.0 (0/1) (0/1) (1/1) -mosdepth 262.0 21.0 mosdepth fast and flexible BAM/CRAM depth calculation To update https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth 0.3.5 mosdepth 0.3.6 (0/1) (0/1) (1/1) -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) -msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) -multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules To update https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea 1.8.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) -multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation Sequencing, Bioinformatics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc 1.11 multiqc 1.19 (1/1) (1/1) (1/1) -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mumer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) -nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments To update https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ 1.41.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) -ncbi_acc_download 5487.0 688.0 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 (1/1) (1/1) (1/1) -ncbi_datasets 3177.0 667.0 datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets 15.19.1 ncbi-datasets-cli (2/2) (0/2) (2/2) -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct 16.2 entrez-direct 16.2 (0/3) (0/3) (0/3) -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils 1.70 python (0/8) (0/8) (8/8) -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (0/1) -necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) -newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) -nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) -ngmlr 1266.0 21.0 ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr 0.2.7 ngmlr 0.2.7 (0/1) (0/1) (1/1) -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils ngsutils 0.5.9 (1/1) (1/1) (1/1) -nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) -novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty 4.3.1 novoplasty 4.3.3 (0/1) (1/1) (1/1) -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) -ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1) -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.4 (0/2) (0/2) (2/2) -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.2 (0/4) (0/4) (4/4) -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18) -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1) -optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) -orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) -pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) -parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) -pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 (0/1) (0/1) (0/1) -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping To update https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 1.10.0 pbmm2 1.13.1 (0/1) (0/1) (0/1) -pe_histogram 4180.0 312.0 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram 1.0.1 openjdk (1/1) (1/1) (1/1) -pear 4305.0 150.0 iuc_pear PEAR evaluates all possible paired-end read overlaps pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear 0.9.6 pear 0.9.6 (1/1) (1/1) (1/1) -pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 (0/1) (0/1) (0/1) (0/1) +baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 (0/2) (0/2) (0/2) (2/2) +braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) (0/1) +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 (0/1) (1/1) (1/1) (1/1) +feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python (0/1) (0/1) (0/1) (0/1) +helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 (0/1) (0/1) (1/1) (1/1) +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) (0/1) +meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 (0/1) (0/1) (0/1) (0/1) +miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl (0/1) (0/1) (0/1) (0/1) +openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 (0/4) (0/4) (0/4) (0/4) +Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests (0/3) (0/3) (3/3) (0/3) +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 (0/1) (0/1) (1/1) (0/1) +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) (0/1) +apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 (1/1) (0/1) (1/1) (0/1) +blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) (0/1) +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) (7/7) +export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX (0/1) (0/1) (0/1) (0/1) +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) (1/1) +gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python (0/1) (0/1) (1/1) (0/1) +hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) (0/1) +hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) (0/1) +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) (0/1) +miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) (1/1) +plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 (0/1) (0/1) (0/1) (0/1) +rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 (0/1) (0/1) (0/1) (0/1) +replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python (0/1) (0/1) (1/1) (0/1) +rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 (0/1) (0/1) (0/1) (0/1) +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 (1/1) (0/1) (1/1) (0/1) +t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) (0/1) +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) (1/1) +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl (0/1) (0/1) (0/1) (0/1) +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) (0/1) +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) (0/1) +biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas (0/1) (0/1) (0/1) (0/1) +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) (1/1) +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk (1/1) (1/1) (1/1) (1/1) +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 (0/1) (0/1) (0/1) (0/1) +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) (0/1) +combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 (0/1) (0/1) (0/1) (0/1) +concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 (0/1) (0/1) (0/1) (0/1) +cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) (0/1) +csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 (0/20) (0/20) (0/20) (1/20) +ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) (0/1) +fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) (0/1) +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) (0/1) +gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 (0/1) (0/1) (0/1) (0/1) +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) (0/1) +kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b1 (0/1) (0/1) (0/1) (0/1) +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) +kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) +mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) (0/1) +mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) (2/2) +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) (0/1) +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base (0/1) (0/1) (0/1) (0/1) +pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python (0/1) (0/1) (0/1) (0/1) +plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r (0/1) (0/1) (0/1) (0/1) +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite (0/1) (0/1) (0/1) (0/1) +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 3.15.5 (0/1) (0/1) (0/1) (0/1) +pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 (0/1) (0/1) (0/1) (0/1) +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python (0/1) (0/1) (0/1) (0/1) +pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) (12/12) +refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) (2/2) +seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) (0/1) +sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 (0/1) (1/1) (1/1) (0/1) +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) (0/1) +spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed (0/1) (0/1) (0/1) (0/1) +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) (0/1) +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred (0/1) (0/1) (0/1) (0/1) +srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) (0/1) +staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) (1/1) +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) (0/1) +tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) (0/1) +camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 (1/2) (2/2) (2/2) (2/2) +correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 (0/1) (0/1) (0/1) (1/1) +gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 (0/1) (0/1) (0/1) (0/1) +genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 (0/1) (0/1) (1/1) (0/1) +influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.2 (0/1) (0/1) (0/1) (1/1) +influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.0.4 (0/1) (0/1) (0/1) (1/1) +ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 (0/2) (0/2) (0/2) (0/2) +isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) (1/1) +kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python (0/1) (0/1) (0/1) (0/1) +mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 (0/1) (0/1) (0/1) (1/1) +ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base (0/1) (0/1) (0/1) (1/1) +nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 (0/1) (0/1) (1/1) (1/1) +nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 (0/1) (0/1) (0/1) (1/1) +nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 (0/2) (2/2) (2/2) (2/2) +normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 (0/1) (1/1) (1/1) (1/1) +physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes To update physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.3.5 physiofit 3.3.6 (0/1) (0/1) (0/1) (1/1) +physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager 1.0.1 (0/1) (0/1) (0/1) (1/1) +skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 (0/1) (0/1) (0/1) (1/1) +xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms 3.12.0 bioconductor-xcms 4.0.0 (9/10) (9/10) (10/10) (10/10) +apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 (0/9) (0/9) (9/9) (0/9) +askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 (0/1) (0/1) (0/1) (0/1) +chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 (0/26) (0/26) (0/26) (0/26) +genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.15 genoboo 0.4.15 (0/1) (0/1) (1/1) (1/1) +jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python (0/1) (0/1) (0/1) (0/1) +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) +tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 (0/22) (0/22) (0/22) (0/22) +w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base (0/1) (1/1) (1/1) (0/1) +w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base (0/1) (1/1) (1/1) (0/1) +w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 (0/1) (1/1) (1/1) (0/1) +batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers batched_lastz richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 (1/1) (0/1) (0/1) (0/1) +ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) +segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.2 segalign-full 0.1.2.2 (1/1) (0/1) (0/1) (0/1) +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +add_value 33763.0 356.0 addValue Add a value as a new column. To update Text Manipulation add_value devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl (1/1) (1/1) (1/1) (1/1) +annotation_profiler 2.0 Annotation_Profiler_0 Profile Annotations for a set of genomic intervals To update Genomic Interval Operations annotation_profiler devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler 1.0.0 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) (1/1) +blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) (0/1) +blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) (0/1) +bowtie_wrappers 22988.0 506.0 bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 (0/1) (1/1) (1/1) (0/1) +canonical_correlation_analysis 72.0 10.0 cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R (0/1) (0/1) (1/1) (1/1) +categorize_elements_satisfying_criteria 40.0 1.0 categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 (0/1) (1/1) (1/1) (0/1) +ccat 165.0 15.0 peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 (0/1) (0/1) (1/1) (0/1) +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) (0/1) +change_case ChangeCase Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl (1/1) (1/1) (1/1) (1/1) +compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) (0/1) +compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) (0/1) +compute_q_values 35.0 compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R (0/1) (0/1) (0/1) (0/1) +condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 (1/1) (1/1) (0/1) (0/1) +convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python (1/1) (1/1) (1/1) (1/1) +convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 (0/1) (0/1) (0/1) (0/1) +correlation 809.0 47.0 cor2 Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy (0/1) (1/1) (1/1) (1/1) +count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) (1/1) +ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) (0/1) +cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) (0/1) +cummerbund_to_tabular 1204.0 13.0 cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 (1/1) (0/1) (1/1) (0/1) +cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 (1/1) (1/1) (1/1) (1/1) +delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) (0/1) +dgidb_annotator 231.0 30.0 dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 (0/1) (0/1) (1/1) (0/1) +divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) (0/1) +draw_stacked_barplots 173.0 12.0 draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R (0/1) (1/1) (1/1) (1/1) +dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_var_perfeature 36.0 dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops (1/1) (1/1) (1/1) (1/1) +express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) (0/1) +fasta_compute_length 7758.0 380.0 fasta_compute_length Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.3 python (1/1) (1/1) (1/1) (1/1) +fasta_concatenate_by_species 35793.0 88.0 fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +fasta_filter_by_length 48649.0 350.0 fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python (1/1) (1/1) (1/1) (1/1) +fasta_to_tabular 105841.0 622.0 fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python (1/1) (1/1) (1/1) (1/1) +fastq_trimmer_by_quality 5485.0 459.0 fastq_quality_trimmer FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 (0/1) (0/1) (0/1) (0/1) +featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) (1/1) +generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) (1/1) +getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) (0/1) +gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) (1/1) +hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) (0/1) +histogram 2367.0 94.0 histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 (1/1) (1/1) (1/1) (1/1) +indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) (0/1) +kernel_canonical_correlation_analysis 69.0 2.0 kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy (1/1) (0/1) (1/1) (1/1) +kernel_principal_component_analysis 155.0 13.0 kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy (1/1) (0/1) (1/1) (1/1) +lastz_paired_reads 9.0 1.0 lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 (0/1) (1/1) (1/1) (0/1) +lda_analysis 148.0 18.0 lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R (1/1) (0/1) (1/1) (1/1) +linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R (1/1) (0/1) (0/1) (0/1) +logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) (0/1) +maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) (0/1) +megablast_xml_parser 338.0 36.0 megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python (1/1) (0/1) (1/1) (0/1) +merge_cols 21906.0 536.0 mergeCols1 Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python (1/1) (1/1) (1/1) (1/1) +microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) (0/1) +microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) (0/1) +microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +mine 11.0 2.0 maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE (1/1) (0/1) (1/1) (1/1) +multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) (0/1) +mutate_snp_codon 47.0 mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 (1/1) (0/1) (1/1) (0/1) +partialr_square partialRsq Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R (1/1) (0/1) (0/1) (0/1) +pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 (0/1) (0/1) (0/1) (0/1) +pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 (0/1) (0/1) (0/1) (0/1) +pileup_interval 632.0 15.0 pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +pileup_parser 3158.0 169.0 pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl (1/1) (1/1) (1/1) (1/1) +plot_from_lda 73.0 9.0 plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R (1/1) (0/1) (1/1) (1/1) +principal_component_analysis 9986.0 88.0 pca1 Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy (1/1) (0/1) (1/1) (1/1) +quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.11.0 (0/1) (0/1) (0/1) (0/1) +rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) (0/1) +remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 (1/1) (1/1) (1/1) (1/1) +rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) (0/1) +rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) (0/1) +sam2interval 1189.0 20.0 sam2interval Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python (1/1) (1/1) (1/1) (1/1) +sam_bitwise_flag_filter 261.0 1.0 sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python (1/1) (1/1) (0/1) (1/1) +scatterplot 1637.0 61.0 scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy (1/1) (0/1) (1/1) (1/1) +short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) (0/1) +short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) (0/1) +short_reads_trim_seq 220.0 21.0 trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 (1/1) (0/1) (1/1) (0/1) +show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 (1/1) (1/1) (1/1) (1/1) +show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 (1/1) (1/1) (1/1) (1/1) +sicer 374.0 5.0 peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 (1/1) (1/1) (1/1) (1/1) +split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 (0/1) (0/1) (0/1) (0/1) +substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) (0/1) +substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +t_test_two_samples 210.0 6.0 t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R (1/1) (1/1) (1/1) (1/1) +table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar (0/1) (0/1) (0/1) (0/1) +tabular_to_fasta 319234.0 601.0 tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python (1/1) (1/1) (1/1) (1/1) +tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 (1/1) (1/1) (1/1) (0/1) +tophat_fusion_post 216.0 15.0 tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ (0/1) (1/1) (1/1) (0/1) +trimmer 6058.0 188.0 trimmer Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 (1/1) (1/1) (1/1) (1/1) +ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) (0/1) +varscan_version_2 5191.0 246.0 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 (1/1) (1/1) (1/1) (1/1) +vcf2pgsnp 206.0 15.0 vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 (1/1) (0/1) (1/1) (0/1) +vcf_annotate 1.0 vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 (0/1) (0/1) (0/1) (0/1) +vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 (0/1) (0/1) (0/1) (0/1) +vcf_filter 388.0 63.0 vcf_filter Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 (0/1) (0/1) (1/1) (0/1) +vcf_intersect 19.0 vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 (0/1) (0/1) (0/1) (0/1) +weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) (0/1) +windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +xy_plot 5890.0 344.0 XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base (1/1) (1/1) (1/1) (1/1) +basecoverage 307.0 2.0 gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +cluster 791.0 1.0 gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +complement 233.0 1.0 gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +concat 564897.0 309.0 gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +coverage 1489.0 17.0 gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +flanking_features 671.0 20.0 flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +get_flanks 324380.0 555.0 get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +intersect 347919.0 1003.0 gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +join 329478.0 284.0 gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +merge 563676.0 193.0 gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +subtract 564149.0 182.0 gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +subtract_query 1014.0 55.0 subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +tables_arithmetic_operations 2207.0 14.0 tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl (0/1) (0/1) (1/1) (1/1) +hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) (0/1) +hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) (0/1) +snpfreq 37.0 7.0 hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R (1/1) (1/1) (1/1) (0/1) +find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk (1/1) (1/1) (1/1) (0/1) +lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 (0/1) (1/1) (1/1) (0/1) +t2ps 457.0 31.0 Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +vcftools_annotate 171.0 24.0 vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo (1/1) (0/1) (1/1) (1/1) +vcftools_compare 531.0 34.0 vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) +vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +vcftools_isec 498.0 35.0 vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 (0/1) (1/1) (1/1) (0/1) +vcftools_merge 953.0 68.0 vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 (0/1) (1/1) (1/1) (0/1) +vcftools_slice 411.0 24.0 vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo (1/1) (0/1) (1/1) (1/1) +vcftools_subset 137.0 17.0 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) +10x_bamtofastq 228.0 46.0 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) (0/1) +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) (0/2) +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) (0/1) +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +agat 481.0 42.0 agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.4.0 (0/1) (0/1) (1/1) (1/1) +antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 (1/1) (1/1) (1/1) (0/1) +atactk_trim_adapters 257.0 26.0 atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 (0/1) (0/1) (1/1) (0/1) +augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) (1/1) +bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) (0/1) +barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools (0/1) (0/1) (1/1) (0/1) +biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 (0/2) (0/2) (2/2) (0/2) +bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) (0/1) +bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (4/4) (4/4) (4/4) +blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) (0/1) +blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) (0/1) +canu 13021.0 533.0 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 (0/1) (1/1) (1/1) (1/1) +cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.8 cellpose (0/1) (0/1) (1/1) (0/1) +cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) +chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) (0/1) +circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) (0/1) +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python (0/1) (0/1) (1/1) (0/1) +compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) (0/1) +cpat 134.0 21.0 cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 (1/1) (1/1) (1/1) (1/1) +crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) (0/1) +diff 235.0 30.0 diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils (1/1) (0/1) (1/1) (0/1) +diffbind 6264.0 250.0 Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind (0/1) (0/1) (0/1) (0/1) +edta 484.0 58.0 edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 (0/1) (0/1) (1/1) (0/1) +epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 (0/1) (0/1) (1/1) (0/1) +fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) (0/1) +file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) (1/1) +find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.4 (1/1) (1/1) (1/1) (1/1) +footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) (0/1) +format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 (0/1) (0/1) (1/1) (0/1) +format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 (0/1) (0/1) (1/1) (0/1) +gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) (0/1) +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) (0/1) +gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) (0/1) +graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 (0/1) (0/1) (0/1) (0/1) +graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) (0/1) +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) (0/2) +hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 (0/1) (0/1) (0/1) (0/1) +hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0.0.12 hictk 0.0.12 (0/1) (0/1) (1/1) (0/1) +hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 (7/7) (0/7) (7/7) (0/7) +hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.9 (1/1) (1/1) (1/1) (1/1) +homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) (0/1) +illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) (0/1) +bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) +graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.43 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) +imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) (0/27) +woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 (0/1) (0/1) (1/1) (0/1) +instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) (0/1) +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) (0/1) +itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) (0/1) +jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 (0/1) (0/1) (0/1) (0/1) +labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) (0/1) +lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 (0/1) (0/1) (1/1) (0/1) +mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.520 mafft 7.525 (2/2) (2/2) (2/2) (2/2) +mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 (0/1) (0/1) (1/1) (0/1) +methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) (0/8) +methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) (0/1) +methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 (0/1) (0/1) (0/1) (1/1) +metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) (1/1) +mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 (0/1) (0/1) (0/1) (0/1) +miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) (0/1) +minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) (0/1) +minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) (0/1) +mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (1/1) (1/1) (0/1) +molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +music_deconvolution 530.0 67.0 music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 (5/5) (5/5) (4/5) (0/5) +nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 (0/4) (4/4) (4/4) (4/4) +netboxr 11.0 5.0 netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 (0/1) (0/1) (1/1) (0/1) +nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) (0/1) +nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) (0/1) +numeric_clustering 486.0 numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda (0/1) (0/1) (0/1) (1/1) +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (7/140) (34/140) (135/140) (0/140) +pandas_rolling_window 269.0 7.0 pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy (1/1) (0/1) (1/1) (0/1) +peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) (0/1) +perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf (0/1) (0/1) (0/1) (0/1) +pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) (1/1) +pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql (0/3) (0/3) (0/3) (0/3) +pharmcat 82.0 14.0 pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat (1/1) (0/1) (1/1) (0/1) +piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) (0/1) +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) (0/1) +plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.3 galaxy-ml 0.10.0 (1/1) (1/1) (1/1) (0/1) +plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) (0/1) +plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) (0/1) +protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) (0/1) +protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) (0/1) +racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) (1/1) +repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 (1/1) (1/1) (1/1) (1/1) +rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 (0/1) (0/1) (0/1) (0/1) +antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) (0/1) +aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) (0/1) +blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) (0/1) +cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl (0/1) (0/1) (1/1) (0/1) +cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) (0/4) +cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) (0/1) +compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 (0/1) (0/1) (1/1) (0/1) +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) (0/1) +dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) (0/1) +dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 (0/1) (0/1) (1/1) (0/1) +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 (0/1) (0/1) (0/1) (0/1) +dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) (0/1) +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) (0/1) +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) (0/1) +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) (0/1) +infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 (0/6) (6/6) (6/6) (0/6) +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) (0/1) +intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) (0/1) +kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) (0/1) +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) (0/5) +mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) (0/1) +mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 (0/1) (0/1) (1/1) (0/1) +nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) (0/1) +paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) (0/1) +pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) (0/1) +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) +rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) +rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) (0/1) +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (1/1) (0/1) +remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) (0/1) +ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) (0/3) +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) (0/1) +rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) (0/1) +rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) (0/1) +rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) (0/1) +rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) (0/1) +rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) (0/1) +rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) (0/6) +selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) (0/1) +sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) (1/1) +sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) (0/1) +targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) (0/1) +trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) (0/2) +vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) (0/23) +sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) (1/1) +salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) +sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_slice, sambamba_sort, sambamba_view, sambamba_depth SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba sambamba 1.0.1 (0/7) (0/7) (0/7) (0/7) +sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed (0/1) (0/1) (0/1) (0/1) +segemehl 1276.0 30.0 segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 (0/1) (0/1) (1/1) (0/1) +sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 (30/33) (14/33) (31/33) (16/33) +splitfasta 1295.0 96.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy (0/1) (0/1) (1/1) (0/1) +stress_ng 47.0 stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng (0/1) (0/1) (0/1) (0/1) +tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) +add_line_to_file 14480.0 193.0 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 (1/1) (1/1) (1/1) (1/1) +join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1) (1/1) +split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1) (1/1) +split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python (1/1) (1/1) (1/1) (1/1) +text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 (20/20) (20/20) (20/20) (20/20) +tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) (0/1) +tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara (0/1) (0/1) (0/1) (0/1) +tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1) (0/1) +trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) +uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.5 requests (1/1) (1/1) (1/1) (0/1) +vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) (0/1) +whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 (0/1) (0/1) (1/1) (0/1) +wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) (1/1) +align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.20 (0/2) (0/2) (0/2) (0/2) +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) (0/1) +count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 (0/1) (0/1) (0/1) (0/1) +fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) (1/1) +mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) (0/1) +nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) (0/1) +predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) (0/1) +protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) (0/6) +sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) (1/1) +seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) (0/1) +venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) (1/1) +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) (0/1) +abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) +abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.7 abyss 2.3.7 (0/1) (1/1) (1/1) (0/1) +adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) (0/1) +add_input_name_as_column 83150.0 91.0 addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python (1/1) (0/1) (1/1) (0/1) +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) (4/4) +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) (0/1) +allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 (0/1) (0/1) (0/1) (0/1) +amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) (0/1) +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.6 (0/19) (0/19) (19/19) (0/19) +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) (1/1) +ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) (0/1) +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.3 anndata 0.6.22.post1 (5/5) (4/5) (5/5) (0/5) +annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) (1/1) +arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) (0/3) +art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (3/3) (0/3) +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) (0/2) +assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) (1/1) +augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) (2/2) +b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) (0/1) +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.3 bakta 1.9.3 (0/1) (1/1) (1/1) (1/1) +bam_to_scidx 128.0 4.0 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) (0/2) +bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) (2/2) +barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 (0/1) (0/1) (0/1) (0/1) +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 (4/4) (0/4) (4/4) (0/4) +barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) (1/1) +basil 266.0 35.0 basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 (1/1) (0/1) (1/1) (0/1) +bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) (0/1) +bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) (0/1) +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) (0/6) +bcftools 524.0 78.0 bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.20 (0/5) (0/5) (0/5) (0/5) +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) (0/7) +beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 (0/3) (0/3) (3/3) (0/3) +beagle 54.0 10.0 beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e (0/1) (0/1) (1/1) (0/1) +bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 (1/1) (0/1) (1/1) (0/1) +bedtools 936832.0 6318.0 bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 (37/37) (37/37) (37/37) (37/37) +bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) (0/1) +berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 (0/1) (1/1) (0/1) (0/1) +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 (0/1) (0/1) (1/1) (0/1) +binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) (0/1) +bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.2 python-bioext 0.21.2 (2/2) (0/2) (2/2) (0/2) +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python (1/1) (0/1) (1/1) (0/1) +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (6/6) (0/6) +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) (1/1) +biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) (0/1) +blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 (0/1) (0/1) (1/1) (0/1) +blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (0/1) +bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 (1/1) (1/1) (1/1) (1/1) +bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (1/1) (1/1) (1/1) (1/1) +breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.38.3 (0/1) (1/1) (1/1) (0/1) +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) +bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 (2/2) (2/2) (2/2) (2/2) +bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) (1/1) +bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) +cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) +calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) (0/1) +calculate_numeric_param 1393.0 8.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 (0/1) (0/1) (1/1) (0/1) +cami_amber cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.4 cami-amber 2.0.4 (0/3) (0/3) (0/3) (0/3) +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) +cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) +cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) (0/1) +charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt (0/1) (0/1) (0/1) (0/1) +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) (10/10) +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) (0/2) +chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.5 (0/8) (0/8) (8/8) (0/8) +chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) (0/5) +chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.8.post1 chopin2 (1/1) (0/1) (0/1) (0/1) +chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) (1/1) +circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) +circos 21787.0 1018.0 circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 (11/11) (11/11) (11/11) (11/11) +cite_seq_count 18.0 1.0 cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.4 (1/1) (0/1) (1/1) (0/1) +clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 0.1.12 clair3 1.0.8 (0/1) (0/1) (1/1) (0/1) +clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) +cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket (0/1) (0/1) (1/1) (0/1) +cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.0.4 cnv-vcf2json (0/1) (0/1) (1/1) (0/1) +cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 (0/17) (0/17) (17/17) (0/17) +codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) +colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) +collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) (1/1) +collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) (1/1) +column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.0 python (1/1) (1/1) (1/1) (1/1) +column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) (1/1) +column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python (1/1) (1/1) (1/1) (1/1) +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) +compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) (1/1) +compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) (0/1) +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis cosg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 (0/1) (0/1) (0/1) (0/1) +coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) (0/1) +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) +crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) (0/1) +crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) (0/1) +crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) (0/7) +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.8 cutadapt 4.8 (1/1) (1/1) (1/1) (1/1) +cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 1.0.8 cutesv 2.1.1 (0/1) (1/1) (1/1) (0/1) +cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) (0/1) +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) +das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 (0/2) (0/2) (2/2) (2/2) +data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python (0/1) (0/1) (0/1) (0/1) +datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 (3/3) (3/3) (3/3) (3/3) +decontaminator 99.0 15.0 decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +deepmicro 501.0 3.0 deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 (0/1) (0/1) (1/1) (0/1) +deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) (1/1) +deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) (0/1) +deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) (1/1) +delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) (0/6) +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) +dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) +diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) (1/1) +dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 (0/1) (0/1) (0/1) (0/1) +disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 (1/1) (0/1) (1/1) (0/1) +dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) (0/1) +dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) (0/1) +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.3.5 dram 1.5.0 (0/5) (0/5) (5/5) (0/5) +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 (0/2) (0/2) (2/2) (2/2) +dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) (1/1) +ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) (0/2) +edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 (1/1) (1/1) (1/1) (1/1) +egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) (0/1) +emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) (107/107) +ena_upload 208.0 14.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). Up-to-date https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.1 ena-upload-cli 0.7.1 (0/1) (1/1) (1/1) (1/1) +enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 (0/5) (0/5) (5/5) (0/5) +ensembl_vep 2653.0 119.0 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 110.1 ensembl-vep 112.0 (0/1) (0/1) (1/1) (0/1) +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 (2/3) (0/3) (3/3) (0/3) +exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) (0/1) +exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) (1/1) +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) (1/1) +extract_genomic_dna 11348.0 285.0 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) (0/1) +fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy (1/1) (1/1) (1/1) (1/1) +fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 (0/1) (0/1) (1/1) (1/1) +fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 (0/1) (0/1) (1/1) (0/1) +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 (1/1) (1/1) (1/1) (1/1) +fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy0 fastqc (1/1) (1/1) (1/1) (1/1) +fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) +fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) +feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (1/1) (1/1) (1/1) +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) (0/2) +fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) (1/1) +filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) (1/1) +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) (0/2) +flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) (0/1) +fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 (0/1) (1/1) (1/1) (1/1) +freebayes 153548.0 3059.0 freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.6 freebayes 1.3.7 (2/2) (2/2) (2/2) (2/2) +freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk (0/1) (0/1) (1/1) (0/1) +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.4.4 freyja 1.5.0 (2/4) (0/4) (4/4) (0/4) +fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib (4/4) (0/4) (0/4) (0/4) +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) (5/5) +gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 (1/1) (0/1) (1/1) (0/1) +gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python (1/1) (0/1) (1/1) (0/1) +gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) (0/1) +gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) (2/3) +genebed_maf_to_fasta 2.0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 (1/1) (1/1) (1/1) (1/1) +genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 (0/1) (0/1) (0/1) (0/1) +geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) (0/1) +genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy (1/1) (0/1) (0/1) (0/1) +genomescope 2118.0 329.0 genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0 genomescope2 2.0 (1/1) (1/1) (1/1) (1/1) +genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) (0/1) +genrich 3515.0 79.0 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 (1/1) (1/1) (1/1) (0/1) +get_hrun 4.0 1.0 get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.1 (0/1) (0/1) (1/1) (0/1) +getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 (0/2) (2/2) (2/2) (0/2) +gfa_to_fa 8274.0 332.0 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 (1/1) (1/1) (1/1) (1/1) +gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (1/1) +gffcompare 3477.0 381.0 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 (1/1) (1/1) (1/1) (1/1) +gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) (1/1) +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) (5/5) +ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset (0/1) (0/1) (0/1) (0/1) +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) (0/8) +goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) (2/2) +goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) (1/1) +gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 (5/5) (0/5) (5/5) (0/5) +graphembed 63.0 2.0 graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 (1/1) (0/1) (1/1) (0/1) +graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 (2/2) (2/2) (2/2) (2/2) +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.3.2 gtdbtk 2.4.0 (0/1) (1/1) (1/1) (0/1) +gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 447 (1/1) (1/1) (1/1) (1/1) +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 (1/1) (1/1) (1/1) (0/1) +gvcftools gvcftools_extract_variants To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 (0/1) (0/1) (0/1) (0/1) +gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) (0/1) +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) +hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 (0/1) (1/1) (0/1) (0/1) +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) +happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) (0/1) +heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.1.3.1 r-gplots 2.17.0 (1/1) (1/1) (1/1) (1/1) +heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.2 hicexplorer 3.7.4 (0/40) (5/40) (40/40) (4/40) +hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.1.5 hicstuff 3.2.2 (0/1) (0/1) (0/1) (0/1) +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) +hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) (1/1) +hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.6.8 (0/1) (0/1) (0/1) (0/1) +hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 (0/12) (12/12) (12/12) (12/12) +homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) (4/5) +htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 (1/1) (1/1) (1/1) (1/1) +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.8 humann 3.8 (6/13) (12/13) (13/13) (13/13) +hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.1.7 (0/1) (1/1) (1/1) (0/1) +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 (17/17) (2/17) (17/17) (2/17) +hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) (0/1) +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 (0/1) (0/1) (0/1) (0/1) +idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) (3/3) +idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) (0/1) +idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.44.1 omero-py 5.11.1 (0/1) (0/1) (1/1) (1/1) +iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) (0/1) +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 (0/2) (0/2) (2/2) (0/2) +integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.3 integron_finder 2.0.3 (0/1) (1/1) (1/1) (1/1) +intermine_galaxy_exchange 44.0 1.0 galaxy_intermine_exchange InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) (1/1) +interval2maf 14.0 3.0 Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +intervene 1497.0 136.0 intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 (2/2) (0/2) (2/2) (0/2) +iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.4 iqtree 2.3.4 (1/1) (1/1) (1/1) (0/1) +irissv 29.0 4.0 irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) (1/1) +isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) (1/1) +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) (5/5) +iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 (3/3) (3/3) (3/3) (0/3) +jasminesv 30.0 3.0 jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 (1/1) (0/1) (1/1) (0/1) +jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) (2/2) +jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.11 (1/1) (1/1) (1/1) (1/1) +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) (1/1) +join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 (0/1) (0/1) (0/1) (0/1) +jq 2312.0 21.0 jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 (1/1) (1/1) (1/1) (1/1) +jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 (1/1) (0/1) (1/1) (0/1) +kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.50.1 (2/2) (2/2) (2/2) (2/2) +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) (0/1) +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) (0/8) +king 5.0 3.0 king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 (0/1) (0/1) (1/1) (0/1) +kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) (0/1) +kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.2.21 kma 1.4.14 (0/1) (0/1) (1/1) (0/1) +kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) (1/1) +kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) (1/1) +kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (1/1) (1/1) (0/1) +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 (1/6) (6/6) (6/6) (6/6) +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (1/1) (0/1) +last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1542 (0/5) (0/5) (5/5) (5/5) +lastz 83331.0 188.0 lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 (2/2) (2/2) (2/2) (2/2) +lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie (0/1) (0/1) (0/1) (0/1) +legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) (0/1) +length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) (1/1) +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) (1/1) +lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base (0/1) (0/1) (1/1) (0/1) +links 405.0 77.0 links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) (0/1) +lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 (5/5) (5/5) (5/5) (4/5) +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) (0/1) +lumpy_sv 358.0 50.0 lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 (0/2) (0/2) (2/2) (0/2) +m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) (0/1) +maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 0.99.12 maaslin2 1.16.0 (0/1) (0/1) (1/1) (0/1) +macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) (9/9) +maf_stats 8.0 2.0 maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 (1/1) (1/1) (1/1) (1/1) +mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 (3/5) (5/5) (5/5) (0/5) +maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) +malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 (0/1) (0/1) (1/1) (0/1) +map_param_value 1528.0 9.0 map_param_value Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 (1/1) (0/1) (1/1) (0/1) +mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) +mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) +mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) +masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) (0/1) +maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) +mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) (3/4) +megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) +megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (0/1) +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_meme, meme_fimo meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) (0/4) +meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) (0/1) +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) +merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) (0/1) +merqury 2483.0 244.0 merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 (2/2) (2/2) (2/2) (2/2) +meryl 6785.0 350.0 meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 (0/7) (0/7) (0/7) (0/7) +metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.15 (2/2) (1/2) (2/2) (2/2) +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) +metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.1 (1/4) (2/4) (4/4) (4/4) +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) +migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) +minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) +miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) +minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 (1/1) (1/1) (1/1) (1/1) +miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) +mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) +mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) +mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) (0/1) +mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 (1/2) (1/2) (2/2) (0/2) +mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) (2/2) +moabs 317.0 19.0 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 (0/1) (0/1) (1/1) (0/1) +mosdepth 262.0 21.0 mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 (0/1) (0/1) (1/1) (0/1) +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) (129/129) +msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) (0/1) +multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) (0/1) +multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.22.2 (1/1) (1/1) (1/1) (1/1) +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) (6/6) +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) +mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) (0/1) +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) (0/3) +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) +nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) +ncbi_acc_download 5487.0 688.0 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 (1/1) (1/1) (1/1) (1/1) +ncbi_datasets 3177.0 667.0 datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.6.0 ncbi-datasets-cli (2/2) (0/2) (2/2) (2/2) +ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 21.6 entrez-direct 21.6 (0/3) (0/3) (0/3) (0/3) +ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python (0/8) (0/8) (8/8) (0/8) +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) +necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) (0/1) +newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) +nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) +ngmlr 1266.0 21.0 ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 (0/1) (0/1) (1/1) (0/1) +ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 (1/1) (1/1) (1/1) (1/1) +nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) (1/1) +novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 (0/1) (1/1) (1/1) (1/1) +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) +ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1) (0/1) +odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.8.6 (0/2) (0/2) (2/2) (2/2) +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4) (0/4) +onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18) (0/18) +optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1) (0/1) +optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) (0/1) +orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) +packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) (0/1) +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 (5/5) (0/5) (5/5) (0/5) +pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) +parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) +pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) +pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 (0/1) (0/1) (0/1) (0/1) +pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.13.1 pbmm2 1.13.1 (0/1) (0/1) (1/1) (0/1) +pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 (1/1) (0/1) (1/1) (0/1) +pe_histogram 4180.0 312.0 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.1 openjdk (1/1) (1/1) (1/1) (1/1) +peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python (0/1) (0/1) (1/1) (0/1) +pear 4305.0 150.0 iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 (1/1) (1/1) (1/1) (0/1) +pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " pharokka - " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " (0/1) (1/1) (1/1) -phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3) -phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) -picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_fastqtosam picard_fastqtosam Create an unaligned BAM file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard 2.18.2 picard 3.1.1 (31/31) (31/31) (31/31) -pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (0/1) (1/1) -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) -pilon 7942.0 467.0 pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon 1.20.1 pilon 1.24 (1/1) (1/1) (1/1) -pipelign 983.0 83.0 pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign 0.2 pipelign 0.2 (1/1) (0/1) (1/1) -pizzly 208.0 16.0 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ 0.37.3.1 pizzly 0.37.3 (1/1) (0/1) (1/1) -plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) -plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) -plink 669.0 46.0 plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink 1.90b6.21 plink 1.90b6.21 (0/1) (0/1) (1/1) -polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) -porechop 185468.0 1046.0 porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop porechop 0.2.4 (1/1) (1/1) (1/1) -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools 0.6.1a1 poretools 0.6.1a1 (13/13) (13/13) (13/13) -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) -pretext pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext 0.1.9 pretextmap 0.1.9 (2/2) (2/2) (2/2) -prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) -progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) -prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) -prot-scriber prot_scriber Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber 0.1.4 prot-scriber 0.1.5 (0/1) (0/1) (1/1) -proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Homology-based gene prediction Phylogeny Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) -psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass 1.0.3 psiclass 1.0.3 (0/1) (0/1) (1/1) -pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) -purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) -pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 5.0.2 pyega3 5.1.0 (1/1) (0/1) (1/1) -pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks 3.8 pygenometracks 3.8 (1/1) (1/1) (1/1) -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/2) (0/2) (2/2) -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/32) (0/32) (32/32) -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (3/4) (4/4) -quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) -query_impc 1.0 query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests (0/1) (0/1) (1/1) -query_tabular 20860.0 168.0 filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.0 python (3/3) (3/3) (3/3) -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 0.2.3 r-raceid 0.1.3 (5/5) (4/5) (5/5) -ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) -rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) -raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) -raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) -rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.6 (0/1) (0/1) (1/1) -read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) -recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.13.2 recentrifuge 1.13.2 (0/1) (0/1) (1/1) -red 578.0 88.0 red Red (REpeat Detector) Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) -repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 matplotlib (1/1) (0/1) (0/1) -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 1.4.2 r-reshape2 (2/2) (0/2) (2/2) -resize_coordinate_window 85.0 5.0 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window 1.0.2 python (1/1) (0/1) (1/1) -rgcca 44.0 3.0 rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca 3.0.2 rgccacmd 3.0.3 (1/1) (0/1) (1/1) -rgrnastar 416677.0 3843.0 rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar 2.7.10b star 2.7.11a (2/2) (2/2) (2/2) -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) -rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast 2.2.3 rnaquast 2.2.3 (0/1) (0/1) (1/1) -roary 12225.0 656.0 roary Roary the pangenome pipeline roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor 3.2.1 rp2biosensor (0/1) (0/1) (0/1) -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths 1.5.1 rp2paths (0/1) (0/1) (0/1) -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign 1.1.1 rpbasicdesign (0/1) (0/1) (0/1) -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba 5.12.3 rptools (0/1) (0/1) (0/1) -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools 5.13.1 rptools (0/5) (0/5) (0/5) -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser 2.5.2 rrparser (0/1) (0/1) (0/1) -rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc 5.0.1 rseqc 5.0.3 (22/22) (22/22) (22/22) -ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa 0.0.8 sansa 0.0.8 (0/1) (0/1) (1/1) -sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) -sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc 0.1.13 sbml2sbol (0/1) (0/1) (0/1) -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (4/5) (5/5) -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ 0.0.7 r-sceasy 0.0.7 (1/1) (0/1) (1/1) -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) -scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) -scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) -seacr 3693.0 50.0 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr 1.3 seacr 1.3 (1/1) (0/1) (1/1) -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 (0/1) (0/1) (0/1) -semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin 2.0.2 semibin 2.0.2 (0/6) (0/6) (6/6) -seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) -seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) -seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.6.1 (0/3) (0/3) (3/3) -seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 1.2.1 seqsero2 1.2.1 (0/1) (0/1) (1/1) -seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) -seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ 0.7.5 seqwish 0.7.9 (0/1) (0/1) (1/1) -seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) -shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) -shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) -sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext 0.0.2 r-argparse 1.0.1 (0/4) (2/4) (4/4) -sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto 0.9.0 sinto 0.10.0 (2/2) (0/2) (2/2) -slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) -sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 (0/1) (0/1) (1/1) -smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) -sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc 1.0.12 sniffles 2.2 (1/1) (1/1) (1/1) -snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) -snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists 0.8.2 snp-dists 0.8.2 (1/1) (1/1) (1/1) -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites 2.5.1 snp-sites 2.5.1 (1/1) (1/1) (1/1) -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff (1/1) (1/1) (1/1) -snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ 1.0 r-base (1/1) (1/1) (1/1) -socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) -sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) -spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) -spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln 2.4.9 python (2/2) (0/2) (2/2) -spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine 2.1 spotyping 2.1 (0/1) (0/1) (1/1) -spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools 3.0.8 sra-tools 3.0.10 (3/3) (3/3) (3/3) -srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 0.2.0 samtools 1.19.2 (0/1) (0/1) (1/1) -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) -star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.12.0 (1/1) (1/1) (1/1) -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model Up-to-date https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.2 (0/3) (0/3) (0/3) -strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka 2.9.10 strelka 2.9.10 (2/2) (0/2) (2/2) -stringtie 167659.0 2165.0 stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie 2.2.1 stringtie 2.2.1 (2/2) (2/2) (2/2) -structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ 1.0 swiftlink 1.0 (0/1) (0/1) (0/1) -syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) -table_compute 208652.0 741.0 table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas (1/1) (1/1) (1/1) -tag_pileup_frequency 164.0 7.0 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency 1.0.2 openjdk (1/1) (0/1) (1/1) -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) -taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler 4.4.1 tb-profiler 5.0.1 (1/1) (1/1) (1/1) -tb_variant_filter 19252.0 209.0 tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 (1/1) (1/1) (1/1) -tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) -tbvcfreport 2290.0 167.0 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport 0.1.10 tbvcfreport 0.1.10 (1/1) (1/1) (1/1) -te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ 1.0.1 samtools 1.19.2 (0/1) (0/1) (1/1) -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) -tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) -tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) -transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 (5/5) (2/5) (5/5) -transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) -trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) -trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (11/13) (13/13) -trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler 0.5.4 trycycler 0.5.4 (0/5) (5/5) (5/5) -tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra 1.1.2 tsebra 1.1.2.2 (0/1) (0/1) (1/1) -tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) -tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l 377 ucsc-blat 445 (0/1) (0/1) (0/1) -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit 377 ucsc-fasplit 377 (1/1) (1/1) (1/1) -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf 448 ucsc-fatovcf 448 (1/1) (0/1) (1/1) -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa 377 ucsc-twobittofa 455 (1/1) (0/1) (1/1) -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig 447 ucsc-wigtobigwig 447 (0/1) (0/1) (1/1) -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 (5/5) (3/5) (5/5) -unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) -usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) -valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet valet 1.0 (1/1) (0/1) (1/1) -vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) -variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) -varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (1/3) (3/3) -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP 1.1.1 varvamp 1.1.1 (0/1) (0/1) (0/1) -vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF Up-to-date Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf 1.6.21 vcf2maf 1.6.21 (0/1) (1/1) (1/1) -vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation To update https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ 0.3.3 vcfanno 0.3.5 (0/1) (0/1) (1/1) -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto 0.17.17 velocyto.py 0.17.17 (1/1) (0/1) (1/1) -velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) -verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko 1.3.1 verkko 1.4.1 (0/1) (0/1) (1/1) -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg 1.23.0 vg 1.54.0 (0/3) (0/3) (3/3) -virhunter 234.0 40.0 virhunter Deep Learning method for novel virus detection in sequencing data virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter 1.0.0 numpy (0/1) (0/1) (1/1) -volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) -vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch 2.8.3 vsearch 2.27.0 (8/8) (8/8) (8/8) -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp 3.0.6 pysam 0.22.0 (0/5) (0/5) (0/5) -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) -weblogo3 2370.0 74.0 rgweblogo3 Sequence Logo generator for fasta weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 3.5.0 weblogo 3.7.9 (1/1) (1/1) (1/1) -windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ 1.0 blast 2.15.0 (0/2) (2/2) (2/2) -winnowmap 248.0 27.0 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap 2.03 winnowmap 2.03 (0/1) (0/1) (1/1) -xpath 234.0 3.0 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) -yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) -zerone 90.0 2.0 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) -bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) -bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) -bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (0/4) (4/4) -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) -cuffcompare 1130.0 65.0 cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffdiff 5831.0 228.0 cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 (1/1) (0/1) (1/1) -cufflinks 32218.0 319.0 cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffmerge 3292.0 122.0 cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffnorm 660.0 27.0 cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffquant 688.0 18.0 cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 (0/1) (1/1) (0/1) -fasta_formatter 2912.0 68.0 cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fasta_nucleotide_changer 774.0 29.0 cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_boxplot 1175.0 51.0 cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_converter 220.0 11.0 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_filter 15153.0 1509.0 cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_to_fasta 13599.0 419.0 cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_artifacts_filter 1809.0 27.0 cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_barcode_splitter 16589.0 128.0 cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_clipper 3321.0 96.0 cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_collapser 61218.0 114.0 cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_nucleotides_distribution 249.0 25.0 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_quality_statistics 2162.0 63.0 cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_renamer 2280.0 68.0 cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_reverse_complement 10831.0 156.0 cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_trimmer 13148.0 205.0 cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_combiner 8676.0 66.0 fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_filter 14222.0 266.0 fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_groomer 94802.0 1028.0 fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_manipulation 2503.0 69.0 fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_masker_by_quality 170.0 16.0 fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_deinterlacer 8410.0 122.0 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_interlacer 17024.0 1087.0 fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_joiner 16635.0 245.0 fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_splitter 3092.0 196.0 fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_stats 4246.0 221.0 fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_to_tabular 12593.0 93.0 fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_trimmer 9757.0 210.0 fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastqtofasta 178172.0 1371.0 fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -tabular_to_fastq 7388.0 200.0 tabular_to_fastq Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ kraken 1.1.1 (5/5) (5/5) (5/5) -kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) -samtools To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools 1.15.1 samtools 1.19.2 (0/1) (0/1) (0/1) -snpeff 101254.0 2843.0 snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff biopython 1.70 (5/5) (5/5) (5/5) -snpsift 5109063.0 1185.0 snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift snpsift 5.2 (8/8) (8/8) (8/8) -snpsift_dbnsfp 46.0 11.0 snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 (1/1) (0/1) (1/1) -snpsift_genesets 390.0 11.0 snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ snpsift 5.2 (1/1) (0/1) (1/1) -vcf2tsv 167913.0 352.0 vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfaddinfo 357.0 8.0 vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfallelicprimitives 15803.0 286.0 vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfannotate 2181.0 77.0 vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfannotategenotypes 192.0 28.0 vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfbedintersect 3217.0 80.0 vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfbreakcreatemulti 471.0 13.0 vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcheck 675.0 39.0 vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcombine 1695.0 99.0 vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcommonsamples 244.0 14.0 vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfdistance 564.0 40.0 vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance vcflib 1.0.9 (1/1) (1/1) (1/1) -vcffilter 44444.0 882.0 vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter vcflib 1.0.9 (1/1) (1/1) (1/1) -vcffixup 917.0 71.0 vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfflatten 177.0 6.0 vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfgeno2haplo 718.0 36.0 vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfgenotypes 451.0 48.0 vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfhethom 1370.0 90.0 vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfleftalign 279.0 10.0 vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfprimers 708.0 12.0 vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfrandomsample 159.0 5.0 vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfselectsamples 854.0 29.0 vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfsort 1852.0 63.0 vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfvcfintersect 972774.0 265.0 vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.9 (1/1) (1/1) (1/1) -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 (0/1) (1/1) (1/1) -appendfdr append_fdr To update appendfdr galaxyp 0.2.0 (0/1) (0/1) (0/1) -bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) -dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) -decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) -dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) -dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) -diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN 1.8.1 (0/1) (1/1) (1/1) -diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) -diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation Up-to-date https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.6 (0/1) (0/1) (1/1) -digestdb digestdb To update digestdb galaxyp 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) -directag_and_tagrecon To update directag_and_tagrecon galaxyp (0/1) (0/1) (0/1) -data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager (0/1) (0/1) (0/1) -data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) -eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (1/3) (3/3) (3/3) -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) -fasta_merge_files_and_filter_unique_sequences 29886.0 461.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python (1/1) (1/1) (1/1) -fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) -feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) -filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) -flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) -gffcompare_to_bed 2115.0 131.0 gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python (1/1) (1/1) (1/1) -hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) -idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) -lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) -ltq_iquant_cli To update ltq_iquant_cli galaxyp (0/1) (0/1) (0/1) -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant 1.22.0 r-base (0/2) (2/2) (2/2) -map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) -maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) -meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) -metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator 1.0.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) -metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) -mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp 1.0.0 mgf-formatter 1.0.0 (0/1) (0/1) (0/1) -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) -morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 287 (0/1) (1/1) (1/1) -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) -msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container To update Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) -msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2023.01.1202 (0/1) (0/1) (1/1) -msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) -msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) -msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) -mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse (0/1) (0/1) (1/1) -mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data To update Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (1/164) (36/164) (160/164) -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) -pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) -pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) -pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) -peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp 1.0.0 python (1/1) (1/1) (1/1) -peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.5 (4/4) (4/4) (4/4) -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) -percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator 3.5 percolator 3.5 (0/4) (4/4) (4/4) -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) -custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db (0/1) (0/1) (0/1) -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp 0.1 (0/5) (0/5) (0/5) -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 (0/1) (0/1) (0/1) -translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) -proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) -proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) -proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) -proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) -proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) -proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) -proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python (0/1) (0/1) (0/1) -protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) -psm_eval psm_eval To update psm_eval galaxyp 0.1.0 binaries_for_psm_eval (0/1) (0/1) (0/1) -psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) -pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.6.3 (0/1) (0/1) (1/1) -quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) -quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) -qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter 0.1.0+galaxy1 geojson (0/1) (0/1) (1/1) -rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) -regex_find_replace 60307.0 495.0 regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python (2/2) (2/2) (2/2) -scaffold scaffold, scaffold_export To update scaffold galaxyp 0.1.0 scaffold (0/2) (0/2) (0/2) -sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) -translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) -unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs 4.5.1 python (1/1) (1/1) (1/1) -uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) -validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 (5/5) (4/5) (5/5) -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.5.2 scipy (4/4) (0/4) (4/4) -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 21.10 ambertools (7/7) (1/7) (7/7) -packmol 288.0 15.0 packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem 18.169.1 packmol (1/1) (0/1) (1/1) -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python (2/2) (0/2) (2/2) -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy (0/1) (0/1) (0/1) -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 (12/15) (7/15) (15/15) -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.0.0 mdanalysis (10/10) (1/10) (10/10) -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter 1.9.7 mdtraj (1/1) (1/1) (1/1) -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer 1.9.9 mdtraj (1/1) (1/1) (1/1) -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.9.7 mdtraj (1/1) (0/1) (1/1) -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer (0/1) (0/1) (1/1) -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd (0/1) (0/1) (0/1) -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.19.2 (0/1) (0/1) (0/1) -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.0 (0/1) (0/1) (0/1) -bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 377 (0/1) (0/1) (0/1) -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python (0/1) (0/1) (0/1) -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) -cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python (0/1) (0/1) (0/1) -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.2 (1/1) (1/1) (1/1) -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.5.2 r-optparse 1.3.2 (0/1) (0/1) (0/1) -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 (0/1) (0/1) (0/1) -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 (0/1) (0/1) (0/1) -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.4.0.0 (0/3) (0/3) (0/3) -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 (0/1) (0/1) (0/1) -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_scran_normalize 78.0 14.0 scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 (0/1) (0/1) (1/1) -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils (0/1) (0/1) (0/1) -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz (0/1) (0/1) (0/1) -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 (0/2) (0/2) (0/2) -manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta 1.6 samtools 1.19.2 (0/1) (0/1) (1/1) -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats 0.19.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.5.1 tar (0/1) (1/1) (0/1) -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs To update http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns 3.4.0+galaxy2 bioconductor-mutationalpatterns 3.12.0 (0/1) (0/1) (0/1) -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/oases 1.3.0 oases 0.2.09 (0/1) (0/1) (0/1) -pathifier 228.0 10.0 pathifier pathifier To update https:// Transcriptomics, Statistics pathifier artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier 1.0.2 r-optparse 1.3.2 (0/1) (0/1) (1/1) -pindel pindel Pindel detects genome-wide structural variation. To update http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel 0.2.5b8+galaxy1 pindel 0.2.5b9 (0/1) (0/1) (0/1) -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage 0.7.0 samtools 1.19.2 (0/1) (0/1) (0/1) -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/nskvir/RepEnrich Transcriptomics, Variant Analysis repenrich artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich 1.5.2 bioconductor-edger 4.0.2 (0/2) (2/2) (0/2) -rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba 0.7.1+galaxy1 sambamba 1.0 (0/1) (1/1) (0/1) -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter 2.2.0 python (0/1) (0/1) (0/1) -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters 1.3.0 pysam 0.22.0 (0/1) (0/1) (0/1) -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures 3.4.2 pysam 0.22.0 (0/2) (0/2) (0/2) -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 (0/2) (0/2) (0/2) -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf 0.1 python (0/1) (0/1) (0/1) -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) -EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/5) (0/5) (5/5) -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy 0.0.2 (0/5) (5/5) (5/5) -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 (0/1) (0/1) (1/1) -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools 0.0.0 r-tangles (0/6) (0/6) (6/6) -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ 2022.3.0 xarray (5/6) (2/6) (6/6) -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) -obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) -ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc 0.0.2 (0/5) (0/5) (5/5) -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) -xmlstarlet 14.0 4.0 xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet 1.6.1 xmlstarlet (0/1) (0/1) (1/1) -c3s 198.0 5.0 c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.1.0 python (1/1) (1/1) (1/1) -cads 52.0 1.0 cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python (0/1) (0/1) (1/1) -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 (0/2) (0/2) (2/2) -cesm 13.0 1.0 cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM 2.1.3 cesm 2.1.3 (0/1) (0/1) (1/1) -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) -eodie 45.0 4.0 eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE 1.0.2 eodie (0/1) (0/1) (1/1) -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python (0/1) (0/1) (1/1) -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald (1/1) (1/1) (1/1) -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python (0/1) (0/1) (1/1) -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python (0/1) (0/1) (0/1) -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.0 (1/1) (1/1) (1/1) -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 (0/1) (0/1) (0/1) -fastq_quality_trimmer 191.0 cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 (0/1) (0/1) (0/1) -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) -decoupler score_genes_aucell, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.4.0+galaxy1 decoupler 1.5.0 (0/2) (0/2) (1/2) -dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy 1.8.1 scanpy-scripts 1.1.6 (17/27) (27/27) (27/27) -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 (0/4) (0/4) (4/4) -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.0.5 r-sceasy 0.0.7 (1/1) (0/1) (1/1) -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.6.3 scmap-cli 0.1.0 (0/7) (0/7) (7/7) -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) -seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.3.0 seurat-scripts 4.0.0 (0/13) (0/13) (12/13) -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml 1.0.0+galaxy1 ucsc-cell-browser 1.2.3 (0/1) (0/1) (1/1) -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.24.0 matchms 0.24.1 (2/13) (9/13) (13/13) -msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.3.0 msmetaenhancer 0.3.0 (0/1) (1/1) (1/1) -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.24.1 (0/1) (0/1) (0/1) -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) -query query Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click (0/1) (0/1) (0/1) -ramclustr 15.0 2.0 ramclustr, ramclustr_define_experiment ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 (2/2) (2/2) (2/2) -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.12.0 r-recetox-aplcms 0.12.0 (0/8) (8/8) (8/8) -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 (0/1) (0/1) (0/1) -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 (0/1) (1/1) (1/1) -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas (0/1) (0/1) (1/1) -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 (0/4) (0/4) (0/4) -riassigner 15.0 3.0 riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.3.4 riassigner 0.3.4 (1/1) (0/1) (1/1) -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python (0/1) (1/1) (1/1) -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 (0/2) (0/2) (0/2) -waveica 6.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 (1/1) (0/1) (1/1) -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb (0/1) (0/1) (1/1) -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy (0/1) (0/1) (0/1) -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml 0.9.3 htslib 1.19.1 (4/4) (0/4) (4/4) -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.12 (0/1) (0/1) (0/1) -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20231220 fiji 20231211 (0/1) (0/1) (0/1) -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.19.2 (1/1) (0/1) (1/1) -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) -blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) -blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) -blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) -ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) + " (0/1) (1/1) (1/1) (0/1) +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) +phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) +picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_reordersam, picard_replacesamheader, picard_fastqtosam picard_samtofastq Create a FASTQ file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31) (31/31) +pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (1/1) (1/1) (0/1) +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) +pilon 7942.0 467.0 pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 (1/1) (1/1) (1/1) (1/1) +pipelign 983.0 83.0 pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 (1/1) (0/1) (1/1) (0/1) +pizzly 208.0 16.0 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 (1/1) (0/1) (1/1) (0/1) +plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) +plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) +plink 669.0 46.0 plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 (1/1) (0/1) (1/1) (1/1) +polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) +porechop 185468.0 1046.0 porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 (1/1) (1/1) (1/1) (0/1) +poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 (13/13) (13/13) (13/13) (0/13) +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) (0/11) +pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 (3/3) (2/3) (3/3) (0/3) +prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) (1/1) +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) +progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) (0/2) +prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) +prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.5 prot-scriber 0.1.5 (0/1) (0/1) (1/1) (0/1) +proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) (0/3) +psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 (0/1) (0/1) (1/1) (0/1) +pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) (0/1) +purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) (0/1) +pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) +pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 (1/1) (0/1) (1/1) (0/1) +pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 (1/1) (1/1) (1/1) (1/1) +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) (0/1) +qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) (0/1) +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 (0/2) (0/2) (2/2) (2/2) +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 (0/32) (0/32) (32/32) (32/32) +qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip (0/1) (0/1) (1/1) (0/1) +qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) (0/1) +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (4/4) (4/4) (1/4) +quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) (1/1) +query_impc 1.0 query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests (0/1) (0/1) (1/1) (0/1) +query_tabular 20860.0 168.0 filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.0 python (3/3) (3/3) (3/3) (1/3) +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) (0/1) +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 (5/5) (5/5) (5/5) (1/5) +ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) (1/1) +rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) (1/1) +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 0.8.0 rasusa 2.0.0 (0/1) (0/1) (1/1) (0/1) +raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 (0/1) (1/1) (1/1) (1/1) +raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) (1/1) +rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 (0/1) (0/1) (1/1) (0/1) +read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) (0/1) +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.14.0 recentrifuge 1.14.0 (0/1) (0/1) (1/1) (1/1) +red 578.0 88.0 red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) (1/1) +repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) (1/1) +repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib (1/1) (0/1) (0/1) (0/1) +reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 (2/2) (0/2) (2/2) (2/2) +resize_coordinate_window 85.0 5.0 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python (1/1) (0/1) (1/1) (0/1) +revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) +rgcca 44.0 3.0 rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 (1/1) (0/1) (1/1) (0/1) +rgrnastar 416677.0 3843.0 rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b (2/2) (2/2) (2/2) (2/2) +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) (0/2) +rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.2.3 rnaquast 2.2.3 (1/1) (0/1) (1/1) (1/1) +roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) +rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor (0/1) (0/1) (0/1) (0/1) +rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths (0/1) (0/1) (0/1) (0/1) +rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign (0/1) (0/1) (0/1) (0/1) +rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools (0/1) (0/1) (0/1) (0/1) +rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools (0/5) (0/5) (0/5) (0/5) +rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser (0/1) (0/1) (0/1) (0/1) +rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing Up-to-date https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.3 (22/22) (22/22) (22/22) (22/22) +ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) (0/1) +salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) (0/1) +samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) (0/1) +sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.1 sansa 0.2.1 (0/1) (0/1) (1/1) (0/1) +sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) +sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) +sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol (0/1) (0/1) (0/1) (0/1) +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) (0/6) +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (5/5) (5/5) (0/5) +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 (1/1) (0/1) (1/1) (0/1) +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) (0/16) +scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) (0/1) +scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) (0/1) +scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) (0/1) +seacr 3693.0 50.0 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 (1/1) (0/1) (1/1) (0/1) +selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 (0/1) (0/1) (0/1) (0/1) +semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 (0/6) (0/6) (6/6) (1/6) +seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) (0/1) +seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) (0/1) +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 (0/5) (2/5) (3/5) (2/5) +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) +seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) (15/15) +seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.10 (0/1) (0/1) (1/1) (0/1) +seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) +shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.12.0 (0/1) (1/1) (1/1) (0/1) +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) +shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) +sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) (1/1) +simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 (0/4) (2/4) (4/4) (0/4) +sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) (0/1) +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.9.0 sinto 0.10.1 (2/2) (0/2) (2/2) (0/2) +slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) (0/2) +sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) (0/1) +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing To update https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.1 (0/1) (0/1) (1/1) (0/1) +smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) (0/1) +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) (0/2) +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Epigenetics, Sequence Analysis snapatac2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.5.3 (0/4) (0/4) (4/4) (0/4) +sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 1.0.12 sniffles 2.3.3 (1/1) (1/1) (1/1) (1/1) +snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) (0/1) +snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) (3/3) +snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 (1/1) (1/1) (1/1) (0/1) +snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 (1/1) (1/1) (1/1) (0/1) +snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 (1/1) (1/1) (1/1) (1/1) +snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base (1/1) (1/1) (1/1) (1/1) +socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) (0/1) +sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) +spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python (2/2) (0/2) (2/2) (0/2) +spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) +spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) +sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.0 sra-tools 3.1.1 (3/3) (3/3) (3/3) (3/3) +srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) (12/13) +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) (12/12) +star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 (1/1) (1/1) (1/1) (0/1) +straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 (0/3) (0/3) (0/3) (0/3) +strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 (2/2) (0/2) (2/2) (0/2) +stringtie 167659.0 2165.0 stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 (2/2) (2/2) (2/2) (2/2) +structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) (1/1) +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) (0/1) +swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 (0/1) (0/1) (0/1) (0/1) +syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) (0/1) +table_compute 208652.0 741.0 table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas (1/1) (1/1) (1/1) (1/1) +tag_pileup_frequency 164.0 7.0 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk (1/1) (0/1) (1/1) (0/1) +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) (1/1) +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction Up-to-date https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.2.1 (1/1) (1/1) (1/1) (0/1) +tb_variant_filter 19252.0 209.0 tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 (1/1) (1/1) (1/1) (0/1) +tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) (1/1) +tbvcfreport 2290.0 167.0 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.0 tbvcfreport 1.0.0 (1/1) (1/1) (1/1) (0/1) +te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) (0/1) +tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) (0/1) +tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) (0/1) +tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.6 tn93 1.0.14 (4/4) (0/4) (4/4) (0/4) +tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.8.5.0 tooldistillator 0.8.5.0 (0/2) (0/2) (2/2) (2/2) +tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.3 tracegroomer 0.1.3 (0/1) (0/1) (1/1) (1/1) +tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) (0/4) +transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) (1/1) +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) +transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) +trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) (1/1) +trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) +trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) +tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.5 (0/1) (0/1) (1/1) (1/1) +tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) (1/1) +tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) (0/1) +ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 377 ucsc-blat 445 (0/1) (0/1) (0/1) (0/1) +fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 377 ucsc-fasplit 377 (1/1) (1/1) (1/1) (1/1) +fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 (1/1) (1/1) (1/1) (0/1) +twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 377 ucsc-twobittofa 455 (1/1) (1/1) (1/1) (0/1) +wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 447 ucsc-wigtobigwig 447 (1/1) (1/1) (1/1) (0/1) +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.2 umi_tools 1.1.5 (5/5) (5/5) (5/5) (5/5) +unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) (1/1) +usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) (0/2) +valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 (1/1) (0/1) (1/1) (1/1) +vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) (0/1) +vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) (0/1) +variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) (0/3) +varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (3/3) (3/3) (3/3) +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.0 (0/1) (0/1) (1/1) (0/1) +vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF To update Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 (0/1) (1/1) (1/1) (0/1) +vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 (0/1) (0/1) (1/1) (0/1) +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3) +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 (1/1) (0/1) (1/1) (0/1) +velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) (2/2) +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) +verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.1 (0/1) (0/1) (1/1) (0/1) +vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.56.0 (0/3) (0/3) (3/3) (3/3) +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) +virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7 virheat 0.7 (0/1) (0/1) (0/1) (0/1) +virhunter 234.0 40.0 virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) (1/1) +vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.28.1 (8/8) (8/8) (8/8) (8/8) +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 (0/5) (0/5) (0/5) (0/5) +weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) (0/1) +weblogo3 2370.0 74.0 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 (1/1) (1/1) (1/1) (1/1) +windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) +winnowmap 248.0 27.0 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 (0/1) (0/1) (1/1) (0/1) +xpath 234.0 3.0 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) (0/1) +yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) (0/1) +zerone 90.0 2.0 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) (0/1) +bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) +bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) (1/1) +bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (2/4) (4/4) (0/4) +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) +cuffcompare 1130.0 65.0 cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffdiff 5831.0 228.0 cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 (1/1) (0/1) (1/1) (0/1) +cufflinks 32218.0 319.0 cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffmerge 3292.0 122.0 cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffnorm 660.0 27.0 cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +cuffquant 688.0 18.0 cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 (0/1) (1/1) (0/1) (0/1) +fasta_formatter 2912.0 68.0 cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fasta_nucleotide_changer 774.0 29.0 cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_boxplot 1175.0 51.0 cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_converter 220.0 11.0 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_filter 15153.0 1509.0 cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_to_fasta 13599.0 419.0 cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_artifacts_filter 1809.0 27.0 cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_barcode_splitter 16589.0 128.0 cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_clipper 3321.0 96.0 cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_collapser 61218.0 114.0 cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_nucleotides_distribution 249.0 25.0 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_quality_statistics 2162.0 63.0 cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_renamer 2280.0 68.0 cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_reverse_complement 10831.0 156.0 cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_trimmer 13148.0 205.0 cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_combiner 8676.0 66.0 fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_filter 14222.0 266.0 fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_groomer 94802.0 1028.0 fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_manipulation 2503.0 69.0 fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_masker_by_quality 170.0 16.0 fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_deinterlacer 8410.0 122.0 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_interlacer 17024.0 1087.0 fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_joiner 16635.0 245.0 fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_splitter 3092.0 196.0 fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_stats 4246.0 221.0 fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_to_tabular 12593.0 93.0 fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_trimmer 9757.0 210.0 fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastqtofasta 178172.0 1371.0 fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (0/1) +tabular_to_fastq 7388.0 200.0 tabular_to_fastq Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) +samtools To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.15.1 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +snpeff 101254.0 2843.0 snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 (5/5) (5/5) (5/5) (5/5) +snpsift 5109063.0 1185.0 snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 (8/8) (8/8) (8/8) (8/8) +snpsift_dbnsfp 46.0 11.0 snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +snpsift_genesets 390.0 11.0 snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +vcf2tsv 167913.0 352.0 vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfaddinfo 357.0 8.0 vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfallelicprimitives 15803.0 286.0 vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfannotate 2181.0 77.0 vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfannotategenotypes 192.0 28.0 vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbedintersect 3217.0 80.0 vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbreakcreatemulti 471.0 13.0 vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcheck 675.0 39.0 vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcombine 1695.0 99.0 vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcommonsamples 244.0 14.0 vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfdistance 564.0 40.0 vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffilter 44444.0 882.0 vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffixup 917.0 71.0 vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfflatten 177.0 6.0 vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgeno2haplo 718.0 36.0 vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgenotypes 451.0 48.0 vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfhethom 1370.0 90.0 vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfleftalign 279.0 10.0 vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib (1/1) (1/1) (1/1) (1/1) +vcfprimers 708.0 12.0 vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfrandomsample 159.0 5.0 vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfselectsamples 854.0 29.0 vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfsort 1852.0 63.0 vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfvcfintersect 972774.0 265.0 vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.4 (0/1) (1/1) (1/1) (0/1) +appendfdr append_fdr To update appendfdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 (0/1) (0/1) (0/1) (0/1) +bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) (0/1) +blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) (0/1) +bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) (0/5) +calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) (0/1) +cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) (11/11) +dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) (1/1) +decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) (0/1) +dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) (0/1) +dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) (0/1) +diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 (0/1) (1/1) (1/1) (0/1) +diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) (0/1) +diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 (0/1) (0/1) (1/1) (0/1) +digestdb digestdb To update digestdb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +directag_and_tagrecon To update directag_and_tagrecon galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon (0/1) (0/1) (0/1) (0/1) +data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper (0/1) (0/1) (0/1) (0/1) +data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) (0/1) +eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (3/3) (3/3) (3/3) (3/3) +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) (0/7) +fasta_merge_files_and_filter_unique_sequences 29886.0 461.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python (1/1) (1/1) (1/1) (1/1) +fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) (0/2) +feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) (0/1) +filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) (1/1) +flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) (0/1) +gffcompare_to_bed 2115.0 131.0 gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python (1/1) (1/1) (1/1) (0/1) +hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) (0/2) +idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) (0/1) +lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) (0/1) +ltq_iquant_cli To update ltq_iquant_cli galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli (0/1) (0/1) (0/1) (0/1) +maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base (0/2) (2/2) (2/2) (2/2) +map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) (0/2) +meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) (0/1) +metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) (0/1) +metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) (0/1) +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) (0/6) +mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 (0/1) (0/1) (0/1) (0/1) +moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) (0/1) +morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 288 (0/1) (1/1) (1/1) (0/1) +mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) (0/2) +msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) (1/1) +msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 (0/1) (0/1) (1/1) (0/1) +msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) (1/1) +msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) (0/1) +msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) (0/1) +mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse (0/1) (0/1) (1/1) (0/1) +mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) (0/1) +openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (8/164) (35/164) (160/164) (0/164) +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) (0/1) +pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) (0/1) +pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) (0/1) +pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) (0/3) +peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python (1/1) (1/1) (1/1) (0/1) +peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.6 (4/4) (4/4) (4/4) (4/4) +pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) (0/1) +percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.6.5 (0/4) (4/4) (4/4) (0/4) +pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) (0/3) +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) (0/1) +custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) (1/1) +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager (0/1) (0/1) (0/1) (0/1) +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) (1/1) +proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 (0/5) (0/5) (0/5) (0/5) +retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 (0/1) (0/1) (0/1) (0/1) +translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) (0/1) +proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python (0/1) (0/1) (0/1) (0/1) +protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +psm_eval psm_eval To update psm_eval galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval (0/1) (0/1) (0/1) (0/1) +psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) (0/1) +pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) (0/6) +pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.2 (0/1) (0/1) (1/1) (0/1) +quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) (1/1) +quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) (0/1) +qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.2.1 geojson (0/1) (0/1) (1/1) (0/1) +rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) (0/1) +regex_find_replace 60307.0 495.0 regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python (2/2) (2/2) (2/2) (2/2) +scaffold scaffold, scaffold_export To update scaffold galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold (0/2) (0/2) (0/2) (0/2) +sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) (0/4) +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python (1/1) (1/1) (1/1) (0/1) +uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) (0/1) +validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) (0/1) +bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 (5/5) (4/5) (5/5) (0/5) +biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy (4/4) (0/4) (4/4) (0/4) +ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools (7/7) (2/7) (7/7) (0/7) +packmol 288.0 15.0 packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol (1/1) (0/1) (1/1) (0/1) +topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python (2/2) (0/2) (2/2) (0/2) +free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy (0/1) (0/1) (0/1) (0/1) +gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 (14/15) (8/15) (15/15) (0/15) +mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis (10/10) (1/10) (10/10) (0/10) +mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj (1/1) (1/1) (1/1) (0/1) +mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj (1/1) (1/1) (1/1) (0/1) +mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj (1/1) (0/1) (1/1) (0/1) +openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer (0/1) (0/1) (1/1) (0/1) +vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd (0/1) (0/1) (0/1) (0/1) +artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) (0/1) +bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 377 (0/1) (0/1) (0/1) (0/1) +blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) (0/1) +blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python (0/1) (0/1) (0/1) (0/1) +blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) (0/1) +blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) (0/1) +cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) (0/1) +cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python (0/1) (0/1) (0/1) (0/1) +concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.2 (1/1) (1/1) (1/1) (0/1) +cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.5.2 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) (0/1) +embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 (0/1) (0/1) (0/1) (0/1) +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 (0/1) (0/1) (0/1) (0/1) +fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 (0/1) (0/1) (0/1) (0/1) +fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) (0/1) +gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 (0/3) (0/3) (0/3) (0/3) +get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_scran_normalize 78.0 14.0 scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 (0/1) (0/1) (1/1) (0/1) +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) (0/1) +high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) (0/1) +justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils (0/1) (0/1) (0/1) (0/1) +justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz (0/1) (0/1) (0/1) (0/1) +lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 (0/2) (0/2) (0/2) (0/2) +manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 (0/1) (0/1) (1/1) (0/1) +mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar (0/1) (1/1) (0/1) (0/1) +mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 (0/1) (0/1) (0/1) (0/1) +oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 (0/1) (0/1) (0/1) (0/1) +pathifier 228.0 10.0 pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 (0/1) (0/1) (1/1) (0/1) +pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 (0/1) (0/1) (0/1) (0/1) +probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 (0/2) (2/2) (0/2) (0/2) +repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 (0/2) (0/2) (0/2) (0/2) +rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) (0/4) +sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 (0/1) (1/1) (0/1) (0/1) +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) (0/1) +sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python (0/1) (0/1) (0/1) (0/1) +small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) (0/1) +small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 (0/2) (0/2) (0/2) (0/2) +snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 (0/2) (0/2) (0/2) (0/2) +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) +sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) +tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) (0/1) +varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python (0/1) (0/1) (0/1) (0/1) +xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) (0/2) +yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) (0/1) +EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) (9/9) +Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/6) (0/6) (6/6) (5/6) +Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) (3/3) +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 (0/5) (5/5) (5/5) (5/5) +ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 (0/1) (0/1) (1/1) (1/1) +aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 (0/1) (0/1) (1/1) (0/1) +champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) (3/3) +consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) (1/1) +data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles (0/6) (0/6) (6/6) (6/6) +xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray (5/6) (2/6) (6/6) (5/6) +gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) (8/8) +interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) (0/1) +medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas (0/1) (0/1) (1/1) (0/1) +obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) (1/2) +ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) (0/1) +ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base (0/1) (0/1) (1/1) (0/1) +ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base (0/1) (0/1) (1/1) (0/1) +regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) (7/7) +sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base (0/1) (0/1) (0/1) (0/1) +spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) (1/1) +srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) (7/7) +stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 (0/5) (0/5) (5/5) (5/5) +vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) (4/4) +xmlstarlet 14.0 4.0 xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet (0/1) (0/1) (1/1) (1/1) +zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base (0/1) (0/1) (1/1) (0/1) +c3s 198.0 5.0 c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.2.0 python (1/1) (1/1) (1/1) (0/1) +cads 52.0 1.0 cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python (0/1) (0/1) (1/1) (0/1) +cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 (0/2) (0/2) (2/2) (0/2) +cesm 13.0 1.0 cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 (0/1) (0/1) (1/1) (0/1) +climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) (0/1) +eodie 45.0 4.0 eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie (0/1) (0/1) (1/1) (0/1) +essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python (0/1) (0/1) (1/1) (0/1) +fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald (1/1) (1/1) (1/1) (0/1) +mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) (0/1) +psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) (0/1) +shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python (0/1) (0/1) (1/1) (0/1) +smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python (0/1) (0/1) (0/1) (0/1) +droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) (0/1) +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) (0/1) +gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 (1/1) (1/1) (1/1) (0/1) +fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 (0/1) (0/1) (0/1) (0/1) +fastq_quality_trimmer 191.0 cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 (0/1) (0/1) (0/1) (0/1) +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) (0/2) +salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) (0/1) +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) (0/8) +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) (0/1) +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) (1/1) +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 (0/3) (0/3) (1/3) (0/3) +dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) (0/2) +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) (0/7) +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) (0/9) +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) (0/7) +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 (17/27) (27/27) (27/27) (0/27) +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) (0/6) +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 (0/4) (0/4) (4/4) (0/4) +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 (1/1) (0/1) (1/1) (0/1) +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 (0/7) (0/7) (7/7) (0/7) +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) (0/4) +seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (14/19) (11/19) +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.6 (0/1) (0/1) (1/1) (0/1) +biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) (1/1) +filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 (0/1) (0/1) (0/1) (0/1) +isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 (0/1) (0/1) (0/1) (0/1) +matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.25.0 matchms 0.25.0 (2/14) (9/14) (13/14) (11/14) +misc use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 (0/1) (0/1) (1/1) (0/1) +msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 (0/1) (1/1) (1/1) (1/1) +msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.25.0 (0/1) (0/1) (0/1) (0/1) +mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) (0/1) +qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 (0/3) (0/3) (3/3) (0/3) +query query Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click (0/1) (0/1) (0/1) (0/1) +ramclustr 15.0 2.0 ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 (2/2) (2/2) (2/2) (2/2) +recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.12.0 r-recetox-aplcms 0.12.0 (0/8) (8/8) (8/8) (8/8) +recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 (0/1) (0/1) (1/1) (1/1) +recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 (0/1) (1/1) (1/1) (1/1) +rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas (0/1) (0/1) (1/1) (0/1) +rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas (0/1) (0/1) (0/1) (0/1) +retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 (0/4) (0/4) (0/4) (0/4) +riassigner 15.0 3.0 riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 (1/2) (0/2) (2/2) (1/2) +rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python (0/1) (1/1) (1/1) (1/1) +spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 (0/2) (0/2) (0/2) (0/2) +waveica 6.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 (1/1) (0/1) (1/1) (1/1) +xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb (0/1) (0/1) (1/1) (1/1) +consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl (0/1) (0/1) (0/1) (0/1) +cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.20 (4/5) (0/5) (5/5) (0/5) +fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 (0/1) (0/1) (0/1) (0/1) +getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) +incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) +measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) +omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.20 (1/1) (0/1) (1/1) (0/1) +upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) +blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) (0/1) +blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) (0/1) +make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) (16/18) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) diff --git a/results/all_tools_wordcloud.png b/results/all_tools_wordcloud.png index 86d269a5..8abfe3ef 100644 Binary files a/results/all_tools_wordcloud.png and b/results/all_tools_wordcloud.png differ diff --git a/results/imaging/index.html b/results/imaging/index.html index 1f3b1ef2..792c7de7 100644 --- a/results/imaging/index.html +++ b/results/imaging/index.html @@ -58,857 +58,105 @@ Expand Galaxy wrapper id - Galaxy wrapper version - Conda version - Conda id - Status + Total tool usage (usegalaxy.eu) + No. of tool users (2022-2023) (usegalaxy.eu) + Galaxy tool ids + Description bio.tool id + bio.tool ids + biii bio.tool name + bio.tool description EDAM operation EDAM topic - Description - bio.tool description Status Source ToolShed categories - ToolShed id - Galaxy wrapper owner - Galaxy wrapper source - - - - - - 2d_auto_threshold - 0.0.5-2 - - scikit-image - To update - scikit-image - scikit-image - Image analysis, Image annotation, Visualisation, Data handling - Imaging, Software engineering, Literature and language - Automatic thresholding - Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. - To update - https://github.com/bmcv - Imaging - 2d_auto_threshold - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ - - - - 2d_feature_extraction - 0.1.1-2 - - pandas - To update - scikit-image - scikit-image - Image analysis, Image annotation, Visualisation, Data handling - Imaging, Software engineering, Literature and language - 2D feature extraction - Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. - To update - https://github.com/bmcv - Imaging - 2d_feature_extraction - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ - - - - 2d_filter_segmentation_by_features - 0.0.1-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - filter segmentation by rules - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - 2d_filter_segmentation_by_features - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ - - - - 2d_histogram_equalization - 0.0.1-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - 2d histogram equalization - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - 2d_histogram_equalization - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ - - - - 2d_simple_filter - 0.0.3-3 - - scikit-image - To update - scikit-image - scikit-image - Image analysis, Image annotation, Visualisation, Data handling - Imaging, Software engineering, Literature and language - 2d simple filter - Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. - To update - https://github.com/bmcv - Imaging - 2d_simple_filter - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ - - - - 3d_tensor_feature_dimension_reduction - 0.0.1 - - numpy - To update - - - - - Dimensionality reduction for features (channels) of 3D tensor data using UMAP - - To update - https://github.com/BMCV/galaxy-image-analysis - Imaging - 3d_tensor_feature_dimension_reduction - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ - - - - anisotropic_diffusion - 0.2-2 - - scikit-image - To update - - - - - Anisotropic image diffusion - - To update - https://github.com/bmcv - Imaging - anisotropic_diffusion - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ - - - - bfconvert - 6.7.0+galaxy2 - 6.7.0 - bftools - To update - - - - - Convert image - - To update - https://github.com/bmcv - Imaging, Convert Formats - bfconvert - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ - - - - binary2labelimage - 0.5 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Binary 2 label image - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - binary2labelimage - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ - - - - binaryimage2points - 0.1-2 - - numpy - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Binary Image to Points - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - binaryimage2points - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ - - - - bioformats2raw - 0.7.0 - - - To update - - - - - Convert image to OME-Zarr - - To update - https://github.com/Euro-BioImaging - Imaging, Convert Formats - bioformats2raw - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw - - - - color-deconvolution - 0.8-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Color-deconvolution methods - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - color_deconvolution - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ - - - - concat_channels - 0.2-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Concatenate images - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - concat_channels - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ - - - - coordinates_of_roi - 0.0.4-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Coordinates of ROI - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - coordinates_of_roi - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ - - - - count_objects - 0.0.5-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Count Objects - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - count_objects - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ - - - - curve_fitting - 0.0.3-2 - - numpy - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Polynomial curve fitting to data points - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/BMCV/galaxy-image-analysis - Imaging - curve_fitting - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ - - - - detection_viz - 0.3-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Detection Visualization - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - detection_viz - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ - - - - image_info - 5.7.1 - 6.7.0 - bftools - To update - - - - - Extracts image metadata - - To update - https://github.com/bmcv - Imaging - image_info - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ - - - - image_registration_affine - 0.0.3-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Intensity-based Image Registration - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - image_registration_affine - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ - - - - imagecoordinates_flipaxis - 0.1-2 - - pandas - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Flip coordinate axes - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - imagecoordinates_flipaxis - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ - - - - labelimage2points - 0.2-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Label Image to Points - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - labelimage2points - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ - - - - landmark_registration - 0.1.0-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Landmark Registration - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - landmark_registration - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ - - - - mahotas-features - 0.7-2 - - mahotas - To update - - - - - Compute image features using mahotas. - - To update - https://github.com/luispedro/mahotas - Imaging - mahotas_features - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ - - - - mergeneighboursinlabelimage - 0.3-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Merge Neighbours in Label Image - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - mergeneighboursinlabelimage - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage - - - - overlay_images - 0.0.4 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Overlay two images - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/BMCV/galaxy-image-analysis - Imaging - overlay_images - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ - - - - permutate_axis - 0.2-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Permutates axes - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - permutate_axis - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ - - - - points2binaryimage - 0.2-1 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Points to Binary Image - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - points2binaryimage - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ - - - - points2labelimage - 0.3-2 - - numpy - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Points to label image - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - points2labelimage - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ - - - - points_association_nn - 0.0.3-2 - - numpy - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Association of points in consecutive frames - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/BMCV/galaxy-image-analysis - Imaging - points_association_nn - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ - - - - projective_transformation - 0.1.2-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Projective transformation - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - projective_transformation - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ - - - - projective_transformation_points - 0.1.1-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Projective transformation of ROIs defined by pixel (point) coordinates - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - projective_transformation_points - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ - - - - rfove - 2023.11.12 - - - To update - rfove - RFOVE - Image analysis - Cell biology, Biomedical science, Imaging - Perform segmentation region-based fitting of overlapping ellipses - RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. - To update - https://sites.google.com/site/costaspanagiotakis/research/cs - Imaging - rfove - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ - - - - scale_image - 0.4-2 - - pillow - To update - scikit-image - scikit-image - Image analysis, Image annotation, Visualisation, Data handling - Imaging, Software engineering, Literature and language - Scale image - Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. - To update - https://github.com/bmcv - Imaging - scale_image - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ - - - - segmetrics - 1.4 - 1.4 - segmetrics - Up-to-date - segmetrics - SegMetrics - Image analysis - - Image segmentation and object detection performance measures - Image segmentation and object detection performance measures - Up-to-date - https://github.com/bmcv - Imaging - segmetrics - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ - - - - slice_image - 0.3-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Slice image - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - slice_image - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ - - - - split_labelmap - 0.2-2 - - scikit-image - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Split Labelmaps - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/bmcv - Imaging - split_labelmap - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ + ToolShed id + Galaxy wrapper owner + Galaxy wrapper source + Galaxy wrapper parsed folder + Galaxy wrapper version + Conda id + Conda version + https://usegalaxy.org + https://usegalaxy.org.au + https://usegalaxy.eu + https://usegalaxy.fr + + - spot_detection_2d - 0.0.3-2 + cellpose - imageio - To update - galaxy_image_analysis - Galaxy Image Analysis - Image analysis - Imaging, Bioinformatics - Spot detection in 2D image sequence - Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. - To update - https://github.com/BMCV/galaxy-image-analysis - Imaging - spot_detection_2d - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ - - - superdsm - 0.1.3 - 0.1.3 - superdsm - Up-to-date - superdsm - SuperDSM - Image analysis + cellpose + Cellpose is an anatomical segmentation algorithm - Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images - SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. - Up-to-date - https://github.com/bmcv - Imaging - superdsm - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ - - - visceral-evaluatesegmentation - 0.5-2 - 2015.07.03 - visceral-evaluatesegmentation - To update - Visceral Project - Evaluate Segmentation Tool To update - https://github.com/bmcv + https://github.com/MouseLand/cellpose Imaging - visceral_evaluatesegmentation - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation - - - - wsi_extract_top_view - 0.2-2 - - scikit-image - To update - - - - - WSI Extract Top View + cellpose + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/cellpose + https://github.com/bgruening/galaxytools/tree/master/tools/cellpose + 3.0.8 + cellpose - To update - https://github.com/bmcv - Imaging - wsi_extract_top_view - imgteam - https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ + (0/1) + (0/1) + (1/1) + (0/1) cellprofiler - - To update + cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects + cellProfiler wrapper CellProfiler CellProfiler + cellprofiler + CellProfiler + Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype - cellProfiler wrapper - Tool for quantifying data from biological images, particularly in high-throughput experiments. To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools + https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler + + + + (0/23) + (23/23) + (23/23) + (19/23) cellprofiler_v4 - 4.2.6 - To update + cp_cellprofiler4 + cellProfiler4 wrapper + + - cellProfiler4 wrapper To update @@ -916,19 +164,28 @@ cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools + https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 + 4.2.6 + + + (0/1) + (0/1) + (1/1) + (1/1) bia-ftplinks - 0.1.0 - wget - To update + + bia_download + Tool to query ftp links for study from bioimage archive + + - Tool to query ftp links for study from bioimage archive To update @@ -936,19 +193,28 @@ bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools + https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks + 0.1.0 + wget + + (0/1) + (0/1) + (1/1) + (0/1) graphicsmagick - 1.3.40 - 1.3.26 - graphicsmagick - To update + + + graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage + Contains tools based on GraphicsMagick + + - Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org @@ -956,59 +222,115 @@ graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ + https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick + 1.3.43 + graphicsmagick + 1.3.26 + (1/3) + (0/3) + (3/3) + (0/3) imagej2 - - To update + imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary + ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. + imagej imagej + imagej2 ImageJ2 + It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging - ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. - It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 + https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 + + + + (0/27) + (0/27) + (27/27) + (0/27) - spyboat - 0.1.2 + woundhealing + + + woundhealing_scratch_assay + Tool to automate quantification of wound healing in high-throughput microscopy scratch assays - spyboat - To update + + + Up-to-date + https://git.embl.de/grp-cba/wound-healing-htm-screen + Imaging + Wound healing scratch assay image analysis + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools + https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing + 1.6.1 + fiji-morpholibj + 1.6.1 + (0/1) + (0/1) + (1/1) + (0/1) + + + + spyboat + 67.0 + 1.0 + spyboat Wavelet analysis for 3d-image stacks + + + + + + To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat + https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat + 0.1.2 + spyboat + + (0/1) + (0/1) + (1/1) + (0/1) qupath_roi_splitter - 0.1.0+galaxy1 + 59.0 + 5.0 + qupath_roi_splitter + Split ROI coordinates of QuPath TMA annotation by cell type + - geojson - To update - Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter @@ -1016,19 +338,28 @@ qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter + 0.2.1 + geojson + + (0/1) + (0/1) + (1/1) + (0/1) hyperstack_to_bleach_corrected_movie - 20230328 - 20231211 - Fiji - To update + + + hyperstack_to_bleach_corrected_movie + Generate blach corrected movie from hyperstack + + - Generate blach corrected movie from hyperstack To update @@ -1036,19 +367,28 @@ hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie + 20230328 + Fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) incucyte_stack_and_upload_omero - 20231221 - 20231211 - Fiji - To update + + + incucyte_stack_and_upload_omero + Combine images to stack and upload to the omero server + + - Combine images to stack and upload to the omero server To update @@ -1056,19 +396,28 @@ incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero + 20231221 + Fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) measure_gastruloids - 20221216 - 20231211 - fiji - To update + + + measureGastruloids + Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index + + - Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update @@ -1076,19 +425,28 @@ measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids + 20221216 + fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) omero_clean_rois_tables - 20230623 - 20231211 - fiji - To update + + + omero_clean_rois_tables + Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down + + - Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update @@ -1096,19 +454,28 @@ omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables + 20230623 + fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) omero_get_children_ids - 0.1.0 - 5.11.1 - omero-py - To update + + + omero_get_children_ids + Get omero id of children of an omero object id + + - Get omero id of children of an omero object id To update @@ -1116,39 +483,86 @@ omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids + 0.1.0 + omero-py + 5.11.1 + (0/1) + (0/1) + (0/1) + (0/1) - omero_hyperstack_to_fluo_measurements_on_gastruloid - 20230809 - 20231211 - fiji + omero_get_full_images + + + omero_get_full_images + Get full images from omero + + + + + + + To update + Imaging + omero_get_full_images + lldelisle + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images + 20240521 + fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) + + + omero_hyperstack_to_fluo_measurements_on_gastruloid + omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels + + + + + + To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid + 20230809 + fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) omero_hyperstack_to_gastruloid_measurements - 20231220 - 20231211 - fiji - To update + + + omero_hyperstack_to_gastruloid_measurements + Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements + + - Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update @@ -1156,19 +570,28 @@ omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements + 20240214 + fiji + 20231211 + (0/1) + (0/1) + (0/1) + (0/1) upload_roi_and_measures_to_omero - 0.0.5 - 5.11.1 - omero-py - To update + + + uploadROIandMeasuresToOMERO + Upload the ROI coordinates and the measurements to the omero server + + - Upload the ROI coordinates and the measurements to the omero server To update @@ -1176,6 +599,14 @@ upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero + https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero + 0.0.5 + omero-py + 5.11.1 + (0/1) + (0/1) + (0/1) + (0/1) diff --git a/results/imaging/tools.tsv b/results/imaging/tools.tsv index 902f25bb..9aa15480 100644 --- a/results/imaging/tools.tsv +++ b/results/imaging/tools.tsv @@ -1,56 +1,19 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu Reviewed To keep -2d_auto_threshold 6541.0 39.0 ip_threshold Automatic thresholding scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) False -2d_feature_extraction 13760.0 19.0 ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ 0.1.1-2 pandas (0/1) (1/1) (1/1) False -2d_filter_segmentation_by_features 6834.0 18.0 ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) False -2d_histogram_equalization 656.0 39.0 ip_histogram_equalization 2d histogram equalization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_histogram_equalization imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) False -2d_simple_filter 6156.0 35.0 ip_filter_standard 2d simple filter scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_simple_filter imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ 0.0.3-3 scikit-image (0/1) (1/1) (1/1) False -3d_tensor_feature_dimension_reduction ip_3d_tensor_feature_dimension_reduction Dimensionality reduction for features (channels) of 3D tensor data using UMAP To update https://github.com/BMCV/galaxy-image-analysis Imaging 3d_tensor_feature_dimension_reduction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ 0.0.1 numpy (0/1) (0/1) (0/1) False -anisotropic_diffusion 40.0 ip_anisotropic_diffusion Anisotropic image diffusion To update https://github.com/bmcv Imaging anisotropic_diffusion imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -bfconvert 1523.0 38.0 ip_convertimage Convert image To update https://github.com/bmcv Imaging, Convert Formats bfconvert imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ 6.7.0+galaxy2 bftools 6.7.0 (0/1) (1/1) (1/1) False -binary2labelimage 1273.0 34.0 ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ 0.5 scikit-image (0/1) (1/1) (1/1) False -binaryimage2points 29.0 ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ 0.1-2 numpy (0/1) (0/1) (1/1) False -bioformats2raw 9.0 bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 (0/1) (0/1) (1/1) False -color-deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ 0.8-2 scikit-image (0/1) (0/1) (1/1) False -concat_channels 78.0 3.0 ip_concat_channels Concatenate images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -coordinates_of_roi 16546.0 8.0 ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ 0.0.4-2 scikit-image (0/1) (0/1) (1/1) False -count_objects 272.0 25.0 ip_count_objects Count Objects galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) False -curve_fitting 12.0 1.0 ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ 0.0.3-2 numpy (0/1) (0/1) (1/1) False -detection_viz 46.0 2.0 ip_detection_viz Detection Visualization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ 0.3-2 scikit-image (0/1) (0/1) (1/1) False -image_info 621.0 41.0 ip_imageinfo Extracts image metadata To update https://github.com/bmcv Imaging image_info imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ 5.7.1 bftools 6.7.0 (0/1) (1/1) (1/1) False -image_registration_affine 12.0 2.0 ip_image_registration Intensity-based Image Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ 0.0.3-2 scikit-image (0/1) (0/1) (1/1) False -imagecoordinates_flipaxis 21825.0 7.0 imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1-2 pandas (0/1) (0/1) (1/1) False -labelimage2points 36.0 ip_labelimage_to_points Label Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -landmark_registration 857.0 9.0 ip_landmark_registration Landmark Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ 0.1.0-2 scikit-image (1/1) (0/1) (1/1) False -mahotas-features ip_mahotas_features Compute image features using mahotas. To update https://github.com/luispedro/mahotas Imaging mahotas_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ 0.7-2 mahotas (0/1) (0/1) (1/1) False -mergeneighboursinlabelimage 25.0 ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage 0.3-2 scikit-image (0/1) (0/1) (1/1) False -overlay_images 60.0 21.0 ip_overlay_images Overlay two images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ 0.0.4 scikit-image (0/1) (0/1) (1/1) False -permutate_axis 42.0 ip_permutate_axis Permutates axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -points2binaryimage 41.0 2.0 ip_points_to_binaryimage Points to Binary Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ 0.2-1 scikit-image (0/1) (0/1) (1/1) False -points2labelimage 66.0 ip_points_to_label Points to label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ 0.3-2 numpy (0/1) (0/1) (1/1) False -points_association_nn 29.0 2.0 ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ 0.0.3-2 numpy (0/1) (0/1) (1/1) False -projective_transformation 44.0 1.0 ip_projective_transformation Projective transformation galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 0.1.2-2 scikit-image (0/1) (0/1) (1/1) False -projective_transformation_points 21208.0 9.0 ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ 0.1.1-2 scikit-image (0/1) (0/1) (1/1) False -rfove 7.0 rfove Perform segmentation region-based fitting of overlapping ellipses rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ 2023.11.12 (0/1) (0/1) (1/1) False -scale_image 615.0 9.0 ip_scale_image Scale image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ 0.4-2 pillow (0/1) (0/1) (1/1) False -segmetrics 3.0 2.0 ip_segmetrics Image segmentation and object detection performance measures segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis Up-to-date https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ 1.4 segmetrics 1.4 (0/1) (0/1) (1/1) False -slice_image 102.0 ip_slice_image Slice image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3-2 scikit-image (0/1) (0/1) (1/1) False -split_labelmap 42.0 ip_split_labelmap Split Labelmaps galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -spot_detection_2d 16.0 3.0 ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ 0.0.3-2 imageio (0/1) (0/1) (1/1) False -superdsm 16.0 2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.1.3 (0/1) (0/1) (1/1) False -visceral-evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 (0/1) (0/1) (1/1) False -wsi_extract_top_view 38.0 ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools (0/23) (23/23) (23/23) False -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.6 (0/1) (0/1) (1/1) False -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools 0.1.0 wget (0/1) (0/1) (1/1) False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.40 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) False -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) False -spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) False -qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter 0.1.0+galaxy1 geojson (0/1) (0/1) (1/1) False -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) False -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) False -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) False -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) False -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) False -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) False -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20231220 fiji 20231211 (0/1) (0/1) (0/1) False -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) False +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr Reviewed To keep +cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.8 cellpose (0/1) (0/1) (1/1) (0/1) False +cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) False +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) False +bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) False +graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.43 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) False +imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) (0/27) False +woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 (0/1) (0/1) (1/1) (0/1) False +spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) False +qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.2.1 geojson (0/1) (0/1) (1/1) (0/1) False +hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) False +omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False +upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) False diff --git a/results/imaging/tools_wordcloud.png b/results/imaging/tools_wordcloud.png index 69023f79..9884ee34 100644 Binary files a/results/imaging/tools_wordcloud.png and b/results/imaging/tools_wordcloud.png differ diff --git a/results/index.html b/results/index.html index 67bd86fa..7a792a6d 100644 --- a/results/index.html +++ b/results/index.html @@ -68,6 +68,7 @@ EDAM topic Description bio.tool description + biii Status Source ToolShed categories @@ -90,6 +91,7 @@ AskoR links EdgeR and AskOmics + To update https://github.com/askomics/askoR Transcriptomics @@ -110,6 +112,7 @@ A data source tool to fetch data from a BARIC Archive server. + To update https://www.cesgo.org/catibaric/ Data Source @@ -130,6 +133,7 @@ BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . + To update https://github.com/Gaius-Augustus/BRAKER Genome annotation @@ -140,7 +144,7 @@ braker3 - 3.0.6 + 3.0.8 To update @@ -150,6 +154,7 @@ BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . + To update https://github.com/Gaius-Augustus/BRAKER Genome annotation @@ -170,6 +175,7 @@ Convert FeelNC GTF to GFF3 + To update https://github.com/tderrien/FEELnc Convert Formats @@ -190,6 +196,7 @@ Conversion from GCMS PostRun Analysis to Isocor + To update Metabolomics @@ -210,6 +217,7 @@ Separate paired and unpaired reads from two fastq files + To update Fastq Manipulation @@ -230,6 +238,7 @@ Gene calling with Deep Neural Networks + To update https://github.com/weberlab-hhu/Helixer Genome annotation @@ -250,6 +259,7 @@ Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence + Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis @@ -270,6 +280,7 @@ Meneco computes minimal completions to your draft network with reactions from a repair network + Up-to-date http://bioasp.github.io/meneco/ Systems Biology @@ -290,6 +301,7 @@ Converts miRanda output into AskOmics format + To update Convert Formats @@ -310,6 +322,7 @@ Creates a summary of several "Internal Standard Report" OpenLabCDS results. + To update Metabolomics @@ -330,6 +343,7 @@ Proteogenomics workflow for the expert annotation of eukaryotic genomes + To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics @@ -350,6 +364,7 @@ A suite of Galaxy tools designed to work with Ensembl REST API. + To update https://rest.ensembl.org Data Source @@ -370,6 +385,7 @@ Gene Align and Family Aggregator + To update http://aequatus.tgac.ac.uk Visualization @@ -390,6 +406,7 @@ TreeBeST best + To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics @@ -410,6 +427,7 @@ Large-scale structural comparison of protein pockets + To update http://cssb.biology.gatech.edu/APoc Computational chemistry @@ -430,6 +448,7 @@ Convert 12- or 24-column BLAST output into 3-column hcluster_sg input + To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics @@ -450,6 +469,7 @@ Analyse phylogenetic trees using the ETE Toolkit + To update http://etetoolkit.org/ Phylogenetics @@ -470,6 +490,7 @@ Export datasets to cluster + To update https://github.com/TGAC/earlham-galaxytools/ Data Export @@ -490,6 +511,7 @@ Gblocks + Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis @@ -510,6 +532,7 @@ GeneSeqToFamily preparation converts data for the workflow + To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats @@ -530,6 +553,7 @@ Hierarchically clustering on a sparse graph + To update https://github.com/douglasgscofield/hcluster Phylogenetics @@ -550,6 +574,7 @@ Converts hcluster_sg 3-column output into lists of ids + To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics @@ -570,6 +595,7 @@ Metagenomics LotuS2 OTU processing pipeline LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. + Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics @@ -590,6 +616,7 @@ Finds potential target sites for miRNAs in genomic sequences + To update http://www.microrna.org/ RNA @@ -610,6 +637,7 @@ This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. + To update Computational chemistry @@ -630,6 +658,7 @@ Docking ligands to proteins and nucleic acids + To update http://rdock.sourceforge.net/ Computational chemistry @@ -650,6 +679,7 @@ Replace chromosome names + To update Text Manipulation @@ -670,6 +700,7 @@ Filter SNPs in RSAT Matrix Scan output + To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology @@ -690,6 +721,7 @@ SMART domains + To update http://smart.embl.de/ Sequence Analysis @@ -710,6 +742,7 @@ smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization + To update https://sourceforge.net/projects/smina/ Computational chemistry @@ -730,6 +763,7 @@ T-Coffee + To update http://www.tcoffee.org/ Sequence Analysis @@ -750,6 +784,7 @@ Order and Orientate Contigs + To update https://github.com/phac-nml/abacas Assembly @@ -770,6 +805,7 @@ Summarise an assembly (e.g. N50 metrics) + To update https://github.com/phac-nml/galaxy_tools Assembly @@ -790,6 +826,7 @@ Generates mapping stats from a bam file. + To update https://github.com/phac-nml/galaxy_tools Assembly @@ -810,6 +847,7 @@ Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. + Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis @@ -830,6 +868,7 @@ Heidelberg and Enteritidis SNP Elucidation + To update https://github.com/phac-nml/biohansel Sequence Analysis @@ -850,6 +889,7 @@ Convert BioHansel output data to a Bionumerics friendly form + To update https://github.com/phac-nml/galaxy_tools Text Manipulation @@ -870,6 +910,7 @@ Tool to bundle up list collection into a single zip to be download + To update Sequence Analysis @@ -890,6 +931,7 @@ Collection tool that collapses a list of files into a single datasset in order of appears in collection + To update Sequence Analysis @@ -910,6 +952,7 @@ JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. + To update Sequence Analysis @@ -930,6 +973,7 @@ Combine multiple Assemblystats datasets into a single tabular report + To update https://github.com/phac-nml/galaxy_tools Assembly @@ -950,6 +994,7 @@ Combine Tabular Collection into a single file + To update Sequence Analysis @@ -970,6 +1015,7 @@ Concatenate paired datasets + To update https://github.com/phac-nml/concat Text Manipulation @@ -990,6 +1036,7 @@ CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. + Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis @@ -1010,6 +1057,7 @@ Rapid data investigation and manipulation of csv/tsv files + To update https://bioinf.shenwei.me/csvtk/ Text Manipulation @@ -1030,6 +1078,7 @@ EC-Typer - in silico serotyping of Escherichia coli species + Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis @@ -1050,6 +1099,7 @@ Convert multiple fasta file into tabular bed file format + To update https://github.com/phac-nml/galaxy_tools Sequence Analysis @@ -1070,6 +1120,7 @@ extract single fasta from multiple fasta file + To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis @@ -1090,6 +1141,7 @@ Summary multiple FastQC into a single tabular line report + To update https://github.com/phac-nml/galaxy_tools Sequence Analysis @@ -1110,6 +1162,7 @@ Automatically identify makers predictive of groups. + To update https://github.com/phac-nml/galaxy_tools Sequence Analysis @@ -1130,6 +1183,7 @@ Remove short and repeat contigs/scaffolds + To update https://github.com/phac-nml/galaxy_tools/ Assembly @@ -1150,6 +1204,7 @@ Download MLST datasets by species from pubmlst.org + To update Sequence Analysis @@ -1170,6 +1225,7 @@ A tool to find nonessential, loss-of-function gene variants + Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis @@ -1190,6 +1246,7 @@ An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. + To update Sequence Analysis @@ -1210,6 +1267,7 @@ Kaptive reports information about capsular (K) loci found in genome assemblies. + To update Sequence Analysis @@ -1230,6 +1288,7 @@ Filtering kmers or reads from a database of kmers hashes + To update Sequence Analysis @@ -1250,6 +1309,7 @@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. + To update @@ -1270,6 +1330,7 @@ Order a draft genome relative to a related reference genome + To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis @@ -1290,6 +1351,7 @@ MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies + To update https://github.com/phac-nml/mob-suite Sequence Analysis @@ -1310,6 +1372,7 @@ A program for the Bayesian estimation of phylogeny. + To update Sequence Analysis @@ -1330,6 +1393,7 @@ RScript to parse the results of mykrobe predictor. + To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis @@ -1350,6 +1414,7 @@ Phylogenetic Assignment of Named Global Outbreak LINeages + To update https://github.com/hCoV-2019/pangolin Sequence Analysis @@ -1370,6 +1435,7 @@ Extract Patristic Distance From a Tree + To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics @@ -1390,6 +1456,7 @@ Explores plasmid content in WGS data + To update @@ -1410,6 +1477,7 @@ Plasmid Profiler suite defining all dependencies for Plasmid Profiler + To update Sequence Analysis @@ -1430,6 +1498,7 @@ Genome assembler for assemblying plasmid + To update Assembly @@ -1450,6 +1519,7 @@ Pneumococcal Capsular Typing of illumina fastq reads + Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis @@ -1470,6 +1540,7 @@ Aligns two sets of contigs and reports amino acid substitutions between them + To update https://github.com/phac-nml/promer Assembly @@ -1490,6 +1561,7 @@ Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. + To update https://github.com/phac-nml/galaxy_tools Sequence Analysis @@ -1510,6 +1582,7 @@ A collection of tools for analysing Viral Quasispecies + Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis @@ -1530,6 +1603,7 @@ Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. + Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis @@ -1550,6 +1624,7 @@ Tool to downsample fastq reads + To update https://github.com/lh3/seqtk Sequence Analysis @@ -1570,6 +1645,7 @@ SISTR in silico serotyping tool + Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis @@ -1590,6 +1666,7 @@ SMALT aligns DNA sequencing reads with a reference genome. + Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis @@ -1610,6 +1687,7 @@ Fixes Spades Fasta ids + To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation @@ -1630,6 +1708,7 @@ Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. + Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis @@ -1650,6 +1729,7 @@ A program for predicting the spoligotype from raw sequence reads + To update Sequence Analysis @@ -1670,6 +1750,7 @@ Short Read Sequence Typing for Bacterial Pathogens + To update Sequence Analysis @@ -1690,6 +1771,7 @@ Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. + Up-to-date https://github.com/phac-nml/staramr Sequence Analysis @@ -1710,6 +1792,7 @@ Rapid and accurate identification of the sequence type (ST) + To update Sequence Analysis @@ -1730,6 +1813,7 @@ Relabels the tips of a newick formatted tree. + To update Text Manipulation @@ -1750,6 +1834,7 @@ identify regions of interest + To update https://github.com/phac-nml/wade Sequence Analysis @@ -1770,6 +1855,7 @@ + To update Metabolomics @@ -1790,6 +1876,7 @@ [Metabolomics][W4M] Metabolites Correlation Analysis + To update http://workflow4metabolomics.org Metabolomics @@ -1810,6 +1897,7 @@ genform: generation of molecular formulas by high-resolution MS and MS/MS data + To update https://sourceforge.net/projects/genform/ Metabolomics @@ -1817,20 +1905,42 @@ workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ + + + influx_data_manager + 1.0.0 + 1.0.0 + influx-si-data-manager + Up-to-date + + + + + Handling influx_si data inputs in Galaxy workflows + + + Up-to-date + https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ + Metabolomics + influx_si_data_manager + workflow4metabolomics + https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager + influx_si 7.0.1 - 7.0.1 + 7.0.2 influx_si - Up-to-date + To update metabolic flux estimation based on [in]stationary labeling - Up-to-date + + To update https://github.com/sgsokol/influx Metabolomics influx_si @@ -1850,6 +1960,7 @@ [W4M][LC-MS] IPO + To update https://github.com/rietho/IPO Metabolomics @@ -1870,6 +1981,7 @@ Isoplot is a software for the visualisation of MS data from C13 labelling experiments + To update Metabolomics, Visualization @@ -1890,6 +2002,7 @@ retrieves data from KMD HMDB API and produce plot and csv file + To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics @@ -1910,6 +2023,7 @@ [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model + To update http://workflow4metabolomics.org Metabolomics @@ -1930,6 +2044,7 @@ [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. + To update http://workflow4metabolomics.org Metabolomics @@ -1950,6 +2065,7 @@ [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation + To update http://workflow4metabolomics.org Metabolomics @@ -1970,6 +2086,7 @@ [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra + To update http://workflow4metabolomics.org Metabolomics @@ -1990,6 +2107,7 @@ [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction + To update http://workflow4metabolomics.org Metabolomics @@ -2010,6 +2128,7 @@ [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data + To update http://workflow4metabolomics.org Metabolomics @@ -2030,6 +2149,7 @@ PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes + Up-to-date physiofit.readthedocs.io Metabolomics @@ -2050,6 +2170,7 @@ Handling of physiofit input files + Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics @@ -2070,6 +2191,7 @@ + To update https://github.com/sneumann/xcms Metabolomics @@ -2090,6 +2212,7 @@ Access an Apollo instance from Galaxy + To update https://github.com/galaxy-genome-annotation/python-apollo Web Services @@ -2110,6 +2233,7 @@ Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ + To update https://github.com/askomics/ Web Services @@ -2130,6 +2254,7 @@ Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado + To update https://github.com/galaxy-genome-annotation/python-chado Web Services @@ -2140,17 +2265,18 @@ genenotebook - 0.4.9 - 0.4.12 + 0.4.13 + 0.4.13 genoboo - To update + Up-to-date Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io - To update + + Up-to-date https://genenotebook.github.io Web Services @@ -2170,6 +2296,7 @@ A tool allowing to export a JBrowse dataset into a JBrowse docker container + To update https://jbrowse.org Web Services @@ -2190,6 +2317,7 @@ Tool for annotation of repeats from unassembled shotgun reads. + To update https://github.com/repeatexplorer/repex_tarean Genome annotation @@ -2210,6 +2338,7 @@ Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal + To update https://github.com/galaxy-genome-annotation/python-tripal Web Services @@ -2230,6 +2359,7 @@ OPLS-DA Contrasts of Univariate Results + To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics @@ -2250,6 +2380,7 @@ Filter W4M data by values or metadata + To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics @@ -2270,6 +2401,7 @@ Join positive- and negative-mode W4M datasets + To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics @@ -2290,6 +2422,7 @@ Imaging, Software engineering, Literature and language Automatic thresholding Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. + scikit-image To update https://github.com/bmcv Imaging @@ -2310,6 +2443,7 @@ Imaging, Software engineering, Literature and language 2D feature extraction Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. + scikit-image To update https://github.com/bmcv Imaging @@ -2330,6 +2464,7 @@ Imaging, Bioinformatics filter segmentation by rules Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2350,6 +2485,7 @@ Imaging, Bioinformatics 2d histogram equalization Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2370,6 +2506,7 @@ Imaging, Software engineering, Literature and language 2d simple filter Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. + scikit-image To update https://github.com/bmcv Imaging @@ -2390,6 +2527,7 @@ Dimensionality reduction for features (channels) of 3D tensor data using UMAP + To update https://github.com/BMCV/galaxy-image-analysis Imaging @@ -2410,6 +2548,7 @@ Anisotropic image diffusion + To update https://github.com/bmcv Imaging @@ -2430,6 +2569,7 @@ Convert image + python-bioformats To update https://github.com/bmcv Imaging, Convert Formats @@ -2450,6 +2590,7 @@ Imaging, Bioinformatics Binary 2 label image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2470,6 +2611,7 @@ Imaging, Bioinformatics Binary Image to Points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2490,6 +2632,7 @@ Convert image to OME-Zarr + To update https://github.com/Euro-BioImaging Imaging, Convert Formats @@ -2510,6 +2653,7 @@ Imaging, Bioinformatics Color-deconvolution methods Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2530,6 +2674,7 @@ Imaging, Bioinformatics Concatenate images Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2550,6 +2695,7 @@ Imaging, Bioinformatics Coordinates of ROI Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2570,6 +2716,7 @@ Imaging, Bioinformatics Count Objects Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2590,6 +2737,7 @@ Send file via cURL POST + To update https://github.com/bmcv Data Export, Web Services @@ -2610,6 +2758,7 @@ Imaging, Bioinformatics Polynomial curve fitting to data points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/BMCV/galaxy-image-analysis Imaging @@ -2630,6 +2779,7 @@ Imaging, Bioinformatics Detection Visualization Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2650,6 +2800,7 @@ Extracts image metadata + python-bioformats To update https://github.com/bmcv Imaging @@ -2670,6 +2821,7 @@ Imaging, Bioinformatics Intensity-based Image Registration Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2690,6 +2842,7 @@ Imaging, Bioinformatics Flip coordinate axes Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2710,6 +2863,7 @@ Imaging, Bioinformatics Label Image to Points Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2730,6 +2884,7 @@ Imaging, Bioinformatics Landmark Registration Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2750,6 +2905,7 @@ Compute image features using mahotas. + mahotas-feature-computation To update https://github.com/luispedro/mahotas Imaging @@ -2770,6 +2926,7 @@ Imaging, Bioinformatics Merge Neighbours in Label Image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2790,6 +2947,7 @@ Imaging, Bioinformatics Overlay two images Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/BMCV/galaxy-image-analysis Imaging @@ -2810,6 +2968,7 @@ Imaging, Bioinformatics Permutates axes Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2830,6 +2989,7 @@ Imaging, Bioinformatics Points to Binary Image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2850,6 +3010,7 @@ Imaging, Bioinformatics Points to label image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2870,6 +3031,7 @@ Imaging, Bioinformatics Association of points in consecutive frames Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/BMCV/galaxy-image-analysis Imaging @@ -2890,6 +3052,7 @@ Imaging, Bioinformatics Projective transformation Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2910,6 +3073,7 @@ Imaging, Bioinformatics Projective transformation of ROIs defined by pixel (point) coordinates Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -2930,6 +3094,7 @@ Cell biology, Biomedical science, Imaging Perform segmentation region-based fitting of overlapping ellipses RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. + To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging @@ -2950,6 +3115,7 @@ Imaging, Software engineering, Literature and language Scale image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. + scikit-image To update https://github.com/bmcv Imaging @@ -2961,16 +3127,17 @@ segmetrics 1.4 - 1.4 + 1.4.1 segmetrics - Up-to-date + To update segmetrics SegMetrics Image analysis Image segmentation and object detection performance measures Image segmentation and object detection performance measures - Up-to-date + segmetrics + To update https://github.com/bmcv Imaging segmetrics @@ -2990,6 +3157,7 @@ Imaging, Bioinformatics Slice image Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -3010,6 +3178,7 @@ Imaging, Bioinformatics Split Labelmaps Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/bmcv Imaging @@ -3030,6 +3199,7 @@ Imaging, Bioinformatics Spot detection in 2D image sequence Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. + To update https://github.com/BMCV/galaxy-image-analysis Imaging @@ -3040,8 +3210,8 @@ superdsm - 0.1.3 - 0.1.3 + 0.2.0 + 0.2.0 superdsm Up-to-date superdsm @@ -3050,6 +3220,7 @@ Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. + superdsm Up-to-date https://github.com/bmcv Imaging @@ -3070,6 +3241,7 @@ Unzip file + To update https://github.com/bmcv Convert Formats @@ -3090,6 +3262,7 @@ Visceral Project - Evaluate Segmentation Tool + evaluatesegmentation-tool To update https://github.com/bmcv Imaging @@ -3110,6 +3283,7 @@ WSI Extract Top View + To update https://github.com/bmcv Imaging @@ -3130,6 +3304,7 @@ Add a value as a new column. + To update Text Manipulation @@ -3141,7 +3316,7 @@ annotation_profiler 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -3150,6 +3325,7 @@ Profile Annotations for a set of genomic intervals + To update Genomic Interval Operations @@ -3170,6 +3346,7 @@ Perform Best-subsets Regression + To update Sequence Analysis, Variant Analysis @@ -3190,6 +3367,7 @@ Polymorphism of the Reads + To update Next Gen Mappers, Sequence Analysis @@ -3210,6 +3388,7 @@ Coverage of the Reads in wiggle format + To update Next Gen Mappers, Sequence Analysis @@ -3230,6 +3409,7 @@ Galaxy wrappers for the Bowtie short read mapping tools. + To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers @@ -3250,6 +3430,7 @@ Canonical Correlation Analysis + To update Statistics @@ -3270,6 +3451,7 @@ Categorize Elements satisfying criteria. + To update Statistics @@ -3290,6 +3472,7 @@ Control-based ChIP-seq Analysis Tool + To update ChIP-seq @@ -3310,6 +3493,7 @@ simple tool for removing duplicates from sequencing reads + To update Metagenomics, Sequence Analysis @@ -3330,6 +3514,7 @@ Convert column case. + To update Text Manipulation @@ -3350,6 +3535,7 @@ Compute Motif Frequencies For All Motifs, motif by motif. + To update Sequence Analysis, Statistics @@ -3370,6 +3556,7 @@ Compute Motif Frequencies in indel flanking regions. + To update Sequence Analysis, Statistics @@ -3390,6 +3577,7 @@ Compute q-values based on multiple simultaneous tests p-values + To update Statistics @@ -3410,6 +3598,7 @@ Condense consecutive characters. + To update Text Manipulation @@ -3430,6 +3619,7 @@ Convert delimiters to tab. + To update Text Manipulation @@ -3450,6 +3640,7 @@ Convert Color Space to Nucleotides + To update Fasta Manipulation @@ -3470,6 +3661,7 @@ Correlation for numeric columns + To update Statistics @@ -3490,6 +3682,7 @@ Count GFF Features + To update Sequence Analysis @@ -3510,6 +3703,7 @@ CTD analysis of chemicals, diseases, or genes + To update Sequence Analysis @@ -3530,6 +3724,7 @@ Wrapper for the Bioconductor cummeRbund library + To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization @@ -3550,6 +3745,7 @@ Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. + To update Convert Formats, Next Gen Mappers @@ -3570,6 +3766,7 @@ Select columns from a dataset. + To update Text Manipulation @@ -3590,6 +3787,7 @@ Delete Overlapping Indels from a chromosome indels file + To update Sequence Analysis @@ -3610,6 +3808,7 @@ Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) + To update Systems Biology, Variant Analysis @@ -3630,6 +3829,7 @@ Separate pgSnp alleles into columns + To update Sequence Analysis @@ -3650,6 +3850,7 @@ Draw Stacked Bar Plots for different categories and different criteria + To update Graphics, Statistics @@ -3670,6 +3871,7 @@ Compute P-values and Correlation Coefficients for Feature Occurrences + To update Statistics @@ -3690,6 +3892,7 @@ Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features + To update Statistics @@ -3710,6 +3913,7 @@ Compute P-values and Second Moments for Feature Occurrences + To update Statistics @@ -3730,6 +3934,7 @@ Compute P-values and Max Variances for Feature Occurrences + To update Statistics @@ -3750,6 +3955,7 @@ Wavelet variance using Discrete Wavelet Transfoms + To update Statistics @@ -3770,6 +3976,7 @@ Quantify the abundances of a set of target sequences from sampled subsequences + To update RNA @@ -3790,6 +3997,7 @@ Compute sequence length + To update Fasta Manipulation @@ -3801,7 +4009,7 @@ fasta_concatenate_by_species 0.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -3810,6 +4018,7 @@ Concatenate FASTA alignment by species + To update Fasta Manipulation @@ -3830,6 +4039,7 @@ Filter sequences by length + To update Fasta Manipulation @@ -3850,6 +4060,7 @@ FASTA-to-Tabular converter + To update Fasta Manipulation @@ -3870,6 +4081,7 @@ FASTQ Quality Trimmer by sliding window + Up-to-date Fastq Manipulation @@ -3890,6 +4102,7 @@ FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data + To update Convert Formats, Fastq Manipulation @@ -3901,7 +4114,7 @@ featurecounter 2.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -3910,6 +4123,7 @@ Feature coverage + To update Sequence Analysis, Variant Analysis @@ -3930,6 +4144,7 @@ Filter Combined Transcripts + To update RNA @@ -3950,6 +4165,7 @@ Generate a Matrix for using PC and LDA + To update Sequence Analysis @@ -3961,7 +4177,7 @@ getindelrates_3way 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -3970,6 +4186,7 @@ Estimate Indel Rates for 3-way alignments + To update Sequence Analysis, Variant Analysis @@ -3990,6 +4207,7 @@ Fetch Indels from pairwise alignments + To update Sequence Analysis, Variant Analysis @@ -4010,6 +4228,7 @@ GMAJ Multiple Alignment Viewer + To update Visualization @@ -4030,6 +4249,7 @@ HISAT is a fast and sensitive spliced alignment program. + To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly @@ -4050,6 +4270,7 @@ Histogram of a numeric column + To update Graphics, Statistics @@ -4070,6 +4291,7 @@ Fetch Indels from 3-way alignments + To update Sequence Analysis @@ -4090,6 +4312,7 @@ Kernel Canonical Correlation Analysis + To update Statistics @@ -4110,6 +4333,7 @@ Kernel Principal Component Analysis + To update Statistics @@ -4130,6 +4354,7 @@ Galaxy wrapper for the Lastz alignment tool on paired reads + To update Next Gen Mappers @@ -4150,6 +4375,7 @@ Perform Linear Discriminant Analysis + To update Graphics, Statistics @@ -4170,6 +4396,7 @@ Perform Linear Regression + To update Statistics @@ -4190,6 +4417,7 @@ Perform Logistic Regression with vif + To update Sequence Analysis, Variant Analysis, Statistics @@ -4201,7 +4429,7 @@ maf_cpg_filter 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -4210,6 +4438,7 @@ Mask CpG/non-CpG sites from MAF file + To update Sequence Analysis, Variant Analysis @@ -4230,6 +4459,7 @@ Format mapping data as UCSC custom track + To update Visualization, Convert Formats, Next Gen Mappers @@ -4250,6 +4480,7 @@ Parse blast XML output + To update Next Gen Mappers, Convert Formats @@ -4270,6 +4501,7 @@ Merge columns together. + To update Text Manipulation @@ -4290,6 +4522,7 @@ Identify microsatellite births and deaths + To update Sequence Analysis @@ -4310,6 +4543,7 @@ Extract Orthologous Microsatellites from pair-wise alignments + To update Sequence Analysis, Variant Analysis @@ -4321,7 +4555,7 @@ microsats_mutability 1.1.0 - 0.10.0 + 0.11.0 bx-python To update @@ -4330,6 +4564,7 @@ Estimate microsatellite mutability by specified attributes + To update Sequence Analysis, Variant Analysis @@ -4350,6 +4585,7 @@ Maximal Information-based Nonparametric Exploration + To update Variant Analysis @@ -4370,6 +4606,7 @@ Extract orthologous microsatellites + To update Sequence Analysis, Variant Analysis @@ -4390,6 +4627,7 @@ Mutate Codons with SNPs + To update Variant Analysis @@ -4410,6 +4648,7 @@ Compute partial R square + To update Statistics @@ -4430,6 +4669,7 @@ Pearson and apos Correlation between any two numeric columns + To update Statistics @@ -4450,6 +4690,7 @@ Convert from pgSnp to gd_snp + To update Variant Analysis @@ -4461,7 +4702,7 @@ pileup_interval 1.0.3 - 0.10.0 + 0.11.0 bx-python To update @@ -4470,6 +4711,7 @@ Pileup-to-Interval condenses pileup format into ranges of bases + To update SAM @@ -4490,6 +4732,7 @@ Filter pileup on coverage and SNPs + To update https://github.com/galaxyproject/tools-devteam/ SAM @@ -4510,6 +4753,7 @@ Draw ROC plot on "Perform LDA" output + To update Graphics, Statistics @@ -4530,6 +4774,7 @@ Principal Component Analysis + To update Statistics @@ -4541,7 +4786,7 @@ quality_filter 1.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -4550,6 +4795,7 @@ Filter nucleotides based on quality scores + To update Sequence Analysis, Variant Analysis @@ -4570,6 +4816,7 @@ Compute RCVE + To update Sequence Analysis, Variant Analysis @@ -4590,6 +4837,7 @@ Remove lines from the beginning of a file. + To update Text Manipulation @@ -4610,6 +4858,7 @@ RMAP for Solexa Short Reads Alignment + To update Next Gen Mappers @@ -4630,6 +4879,7 @@ RMAPQ for Solexa Short Reads Alignment with Quality Scores + To update Next Gen Mappers @@ -4650,6 +4900,7 @@ Convert SAM to interval. + To update SAM @@ -4670,6 +4921,7 @@ Filter SAM on bitwise flag values + To update SAM @@ -4690,6 +4942,7 @@ Scatterplot of two numeric columns + To update Graphics, Statistics @@ -4710,6 +4963,7 @@ Histogram of high quality score reads + To update Sequence Analysis, Graphics @@ -4730,6 +4984,7 @@ Build base quality distribution + To update Sequence Analysis, Graphics @@ -4750,6 +5005,7 @@ Select high quality segments + To update Fastq Manipulation @@ -4770,6 +5026,7 @@ Select lines from the beginning of a file. + To update Text Manipulation @@ -4790,6 +5047,7 @@ Select lines from the end of a file. + To update Text Manipulation @@ -4810,6 +5068,7 @@ Statistical approach for the Identification of ChIP-Enriched Regions + Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq @@ -4830,6 +5089,7 @@ Split paired end reads + To update Fastq Manipulation @@ -4850,6 +5110,7 @@ Estimate substitution rates for non-coding regions + To update Sequence Analysis, Variant Analysis @@ -4861,7 +5122,7 @@ substitutions 1.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -4870,6 +5131,7 @@ Fetch substitutions from pairwise alignments + To update Sequence Analysis, Variant Analysis @@ -4890,6 +5152,7 @@ T Test for Two Samples + To update Statistics @@ -4910,6 +5173,7 @@ Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered + To update Variant Analysis @@ -4930,6 +5194,7 @@ Tabular-to-FASTA + To update Convert Formats @@ -4950,6 +5215,7 @@ Tophat for Illumina + To update RNA, Next Gen Mappers @@ -4970,6 +5236,7 @@ Tophat - fast splice junction mapper for RNA-Seq reads + To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers @@ -4990,6 +5257,7 @@ Wrapper for Tophat-Fusion post step + To update Transcriptomics @@ -5010,6 +5278,7 @@ Trim leading or trailing characters. + To update Text Manipulation @@ -5030,6 +5299,7 @@ Build custom track for UCSC genome browser + To update Sequence Analysis @@ -5050,6 +5320,7 @@ VarScan wrapper + To update https://dkoboldt.github.io/varscan/ Variant Analysis @@ -5070,6 +5341,7 @@ VCF to pgSnp + To update Variant Analysis @@ -5090,6 +5362,7 @@ Annotate a VCF file (dbSNP, hapmap) + To update Variant Analysis @@ -5110,6 +5383,7 @@ Extract reads from a specified region + To update Variant Analysis @@ -5130,6 +5404,7 @@ Filter a VCF file + To update Variant Analysis @@ -5150,6 +5425,7 @@ Generate the intersection of two VCF files + To update Variant Analysis @@ -5170,6 +5446,7 @@ Assign weighted-average of the values of features overlapping an interval + To update Sequence Analysis, Variant Analysis @@ -5181,7 +5458,7 @@ windowsplitter 1.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -5190,6 +5467,7 @@ Make windows + To update Sequence Analysis, Variant Analysis @@ -5210,6 +5488,7 @@ Plotting tool for multiple series and graph types + To update Graphics, Statistics @@ -5221,7 +5500,7 @@ basecoverage 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5230,6 +5509,7 @@ Base Coverage of all intervals + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5241,7 +5521,7 @@ cluster 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5250,6 +5530,7 @@ Cluster the intervals of a dataset + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5261,7 +5542,7 @@ complement 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5270,6 +5551,7 @@ Complement intervals of a dataset + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5281,7 +5563,7 @@ concat 1.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -5290,6 +5572,7 @@ Concatenate two bed files + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5301,7 +5584,7 @@ coverage 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5310,6 +5593,7 @@ Coverage of a set of intervals on second set of intervals + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5321,7 +5605,7 @@ flanking_features 4.0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -5330,6 +5614,7 @@ Fetch closest non-overlapping feature for every interval + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5341,7 +5626,7 @@ get_flanks 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5350,6 +5635,7 @@ Get flanks returns flanking region/s for every gene + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5361,7 +5647,7 @@ intersect 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5370,6 +5656,7 @@ Intersect the intervals of two datasets + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5381,7 +5668,7 @@ join 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5390,6 +5677,7 @@ Join the intervals of two datasets side-by-side + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5401,7 +5689,7 @@ merge 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5410,6 +5698,7 @@ Merge the overlapping intervals of a dataset + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5421,7 +5710,7 @@ subtract 1.0.0 - 0.10.0 + 0.11.0 bx-python To update @@ -5430,6 +5719,7 @@ Subtract the intervals of two datasets + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5441,7 +5731,7 @@ subtract_query 0.1 - 0.10.0 + 0.11.0 bx-python To update @@ -5450,6 +5740,7 @@ Subtract Whole Dataset from another dataset + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5470,6 +5761,7 @@ Arithmetic Operations on tables + To update https://github.com/galaxyproject/gops Genomic Interval Operations @@ -5490,6 +5782,7 @@ FunDO human genes associated with disease terms + To update Sequence Analysis @@ -5510,6 +5803,7 @@ HVIS visualization of genomic data with the Hilbert curve + To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization @@ -5530,6 +5824,7 @@ snpFreq significant SNPs in case-control data + To update Variant Analysis, Statistics @@ -5541,7 +5836,7 @@ find_diag_hits 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -5550,6 +5845,7 @@ Find diagnostic hits + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5561,7 +5857,7 @@ gi2taxonomy 1.1.1 - 0.9.0 + 0.10.0 taxonomy To update @@ -5570,6 +5866,7 @@ Fetch taxonomic representation + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5590,6 +5887,7 @@ Convert Kraken output to Galaxy taxonomy data. + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5601,7 +5899,7 @@ lca_wrapper 1.0.1 - 0.9.0 + 0.10.0 taxonomy To update @@ -5610,6 +5908,7 @@ Find lowest diagnostic rank + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5621,7 +5920,7 @@ poisson2test 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -5630,6 +5929,7 @@ Poisson two-sample test + To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics @@ -5641,7 +5941,7 @@ t2ps 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -5650,6 +5950,7 @@ Draw phylogeny + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5661,7 +5962,7 @@ t2t_report 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -5670,6 +5971,7 @@ Summarize taxonomy + To update https://bitbucket.org/natefoo/taxonomy Metagenomics @@ -5690,6 +5992,7 @@ Annotate VCF using custom/user-defined annotations + To update https://vcftools.github.io/ Variant Analysis @@ -5710,6 +6013,7 @@ Compare VCF files to get overlap and uniqueness statistics + To update https://vcftools.github.io/ Variant Analysis @@ -5730,6 +6034,7 @@ Apply VCF variants to a fasta file to create consensus sequence + To update https://vcftools.github.io/ Variant Analysis @@ -5750,6 +6055,7 @@ Intersect multiple VCF datasets + To update https://vcftools.github.io/ Variant Analysis @@ -5770,6 +6076,7 @@ Merge multiple VCF datasets into a single dataset + To update https://vcftools.github.io/ Variant Analysis @@ -5790,6 +6097,7 @@ Subset VCF dataset by genomic regions + To update https://vcftools.github.io/ Variant Analysis @@ -5810,6 +6118,7 @@ Select samples from a VCF dataset + To update https://vcftools.github.io/ Variant Analysis @@ -5830,6 +6139,7 @@ Converts 10x Genomics BAM to FASTQ + Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats @@ -5850,6 +6160,7 @@ Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. + Up-to-date RNA @@ -5870,6 +6181,7 @@ Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. + To update RNA @@ -5890,6 +6202,7 @@ Determines consensus motives for sequences. + To update RNA @@ -5910,6 +6223,7 @@ Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. + To update RNA @@ -5930,6 +6244,7 @@ Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. + To update RNA @@ -5950,6 +6265,7 @@ Second step of GraphClust + To update RNA @@ -5970,6 +6286,7 @@ MLocARNA computes a multiple sequence-structure alignment of RNA sequences. + To update RNA @@ -5990,6 +6307,7 @@ Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. + To update RNA @@ -6010,6 +6328,7 @@ Plotting results for GraphClust + To update RNA @@ -6030,6 +6349,7 @@ This tool prepares files for locarna step. + To update RNA @@ -6050,6 +6370,7 @@ Preprocessing input for GraphClust + To update RNA @@ -6070,6 +6391,7 @@ Convert RNA structure to GSPAN graphs + To update RNA @@ -6081,16 +6403,17 @@ agat 1.2.0 - 1.2.0 + 1.3.0 agat - Up-to-date + To update agat AGAT Data handling, Genome annotation Genomics GTF/GFF analysis toolkit Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. - Up-to-date + + To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat @@ -6101,16 +6424,17 @@ antismash 6.1.1 - 6.1.1 + 7.1.0 antismash - Up-to-date + To update antismash antiSMASH Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. - Up-to-date + + To update https://antismash.secondarymetabolites.org Sequence Analysis antismash @@ -6130,6 +6454,7 @@ Trim adapters from paired-end HTS reads. + To update https://github.com/ParkerLab/atactk/ Fastq Manipulation @@ -6150,6 +6475,7 @@ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. + To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis @@ -6170,6 +6496,7 @@ Hash BAM and FASTQ files to verify data integrity + Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis @@ -6190,6 +6517,7 @@ Paired End randomer aware duplicate removal algorithm + To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis @@ -6210,6 +6538,7 @@ Convert from bigWig to bedGraph format + To update Convert Formats @@ -6230,6 +6559,7 @@ Random Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts + To update https://www.ebi.ac.uk/biomodels/BIOMD0000001066 Machine Learning @@ -6250,6 +6580,7 @@ Bionano Solve is a set of tools for analyzing Bionano data + To update https://bionanogenomics.com/ Assembly @@ -6270,6 +6601,7 @@ A tool to map bisulfite converted sequence reads and determine cytosine methylation states + To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers @@ -6290,6 +6622,7 @@ Identification and isolation non-target data in draft and publicly available genome assemblies. + To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly @@ -6310,6 +6643,7 @@ Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. + To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis @@ -6330,6 +6664,7 @@ Genomics Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. + Up-to-date https://github.com/marbl/canu @@ -6337,6 +6672,27 @@ bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu + + + cellpose + 3.0.1 + + + To update + + + + + Cellpose is an anatomical segmentation algorithm + + + To update + https://github.com/MouseLand/cellpose + Imaging + cellpose + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/cellpose + cellprofiler @@ -6350,6 +6706,7 @@ Imaging, Microarray experiment, Genotype and phenotype cellProfiler wrapper Tool for quantifying data from biological images, particularly in high-throughput experiments. + cellprofiler To update Imaging @@ -6370,6 +6727,7 @@ cellProfiler4 wrapper + To update Imaging @@ -6390,6 +6748,7 @@ A tool for ChIP peak annotation and visualization + To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation @@ -6410,6 +6769,7 @@ A combined strategy to identify circular RNAs (circRNAs and ciRNAs) + To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA @@ -6430,6 +6790,7 @@ Metagenomics, Molecular interactions, pathways and networks Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances "This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapper + To update Metagenomics @@ -6450,6 +6811,7 @@ Metagenomics, Gene and protein families Compare outputs of HUMAnN2 for several samples and extract similar and specific information "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples." - Galaxy tool wrapper + To update Metagenomics @@ -6460,8 +6822,8 @@ cpat - 3.0.4 - 3.0.4 + 3.0.5 + 3.0.5 cpat Up-to-date @@ -6470,6 +6832,7 @@ Coding-potential assessment tool using an alignment-free logistic regression model. + Up-to-date https://github.com/liguowang/cpat Transcriptomics @@ -6490,6 +6853,7 @@ CRISPR Recognition Tool + To update Sequence Analysis @@ -6510,6 +6874,7 @@ GNU diff tool that calculates the differences between two files. + To update http://www.gnu.org/software/diffutils/ Text Manipulation @@ -6530,6 +6895,7 @@ Diffbind provides functions for processing ChIP-Seq data. + To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq @@ -6550,6 +6916,7 @@ Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. + To update https://github.com/oushujun/EDTA Variant Analysis @@ -6570,6 +6937,7 @@ EpiCSeg is a tool for conducting chromatin segmentation. + To update https://github.com/lamortenera/epicseg Epigenetics @@ -6590,6 +6958,7 @@ FASTQ info allows to validate single or paired fastq files + To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation @@ -6610,6 +6979,7 @@ This tool returns all unique lines from a tab-separated file. + To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation @@ -6630,6 +7000,7 @@ + To update @@ -6640,17 +7011,18 @@ flye - 2.9.1 + 2.9.3 2.9.3 flye - To update + Up-to-date Assembly of long and error-prone reads. - To update + + Up-to-date https://github.com/fenderglass/Flye/ Assembly flye @@ -6670,6 +7042,7 @@ Find transcription factor footprints + To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics @@ -6690,6 +7063,7 @@ Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file + To update Fasta Manipulation @@ -6710,6 +7084,7 @@ Taxonomy, Metagenomics Format MetaPhlAn2 output to extract abundance at different taxonomic levels "This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)." - Galaxy tool wrapper + To update Metagenomics @@ -6730,6 +7105,7 @@ Computational biology Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. + Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis @@ -6750,6 +7126,7 @@ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) + To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis @@ -6770,6 +7147,7 @@ Find subsequences in db + To update Sequence Analysis @@ -6790,6 +7168,7 @@ Convert between different graph formats + To update Convert Formats @@ -6810,6 +7189,7 @@ GraphClust can be used for structural clustering of RNA sequences. + To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA @@ -6830,6 +7210,7 @@ Mapper for long, error-prone reads. + To update https://github.com/isovic/graphmap/ Assembly @@ -6850,6 +7231,7 @@ Plots heatmaps + To update https://bitbucket.org/nsegata/hclust2/ Data Visualization @@ -6857,6 +7239,27 @@ rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 + + + hictk + 0.0.8 + 0.0.9 + hictk + To update + + + + + hictk, a blazing-fast toolkit to work with .hic and .cool files + + + To update + https://github.com/paulsengroup/hictk + + hictk + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/hictk + hicup @@ -6870,6 +7273,7 @@ The HiCUP-Pipeline from the Bioinformatics Babraham Institute. + To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics @@ -6890,6 +7294,7 @@ A fast haplotype-resolved de novo assembler + Up-to-date https://github.com/chhylp123/hifiasm Assembly @@ -6910,6 +7315,7 @@ Software for motif discovery and next generation sequencing analysis. + To update http://homer.salk.edu/homer/ Sequence Analysis @@ -6930,6 +7336,7 @@ Methylation analyzer for Illumina 450k DNA emthylation microarrays + To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis @@ -6950,6 +7357,7 @@ Tool to query ftp links for study from bioimage archive + To update Imaging @@ -6960,7 +7368,7 @@ graphicsmagick - 1.3.40 + 1.3.42 1.3.26 graphicsmagick To update @@ -6970,6 +7378,7 @@ Contains tools based on GraphicsMagick + To update http://www.graphicsmagick.org Imaging @@ -6990,6 +7399,7 @@ Imaging ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. + imagej2 To update http://fiji.sc Imaging @@ -6997,6 +7407,27 @@ imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 + + + woundhealing + 1.6.1 + 1.6.1 + fiji-morpholibj + Up-to-date + + + + + Tool to automate quantification of wound healing in high-throughput microscopy scratch assays + + + Up-to-date + https://git.embl.de/grp-cba/wound-healing-htm-screen + Imaging + Wound healing scratch assay image analysis + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools + instagraal @@ -7010,6 +7441,7 @@ Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites Large genome reassembly based on Hi-C data Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) + To update https://github.com/koszullab/instaGRAAL Assembly @@ -7030,6 +7462,7 @@ Interproscan queries the interpro database and provides annotations. + To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis @@ -7050,6 +7483,7 @@ Functional, regulatory and non-coding RNA, Microbiology ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. + Up-to-date https://microbiology.se/software/itsx/ Metagenomics @@ -7070,6 +7504,7 @@ Run jupyter notebook script in Galaxy + To update Machine Learning @@ -7090,6 +7525,7 @@ remaps and annotates alignments + To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis @@ -7110,6 +7546,7 @@ Lighter is a kmer-based error correction method for whole genome sequencing data + To update Sequence Analysis, Fasta Manipulation @@ -7130,6 +7567,7 @@ Sequence analysis Multiple alignment program for amino acid or nucleotide sequences MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. + To update RNA @@ -7150,6 +7588,7 @@ data source for MaveDB + To update Data Source @@ -7170,6 +7609,7 @@ Markov Cluster Algorithm + To update http://micans.org/mcl/ Sequence Analysis, Metagenomics @@ -7190,6 +7630,7 @@ tools for methylation analysis + To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis @@ -7210,6 +7651,7 @@ A tool for processing bisulfite sequencing alignments + To update https://github.com/dpryan79/MethylDackel Sequence Analysis @@ -7230,6 +7672,7 @@ A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. + To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics @@ -7250,6 +7693,7 @@ Differential DNA methylation calling + To update RNA, Statistics @@ -7270,6 +7714,7 @@ Identification of binding sites in CLIP-Seq data. + To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis @@ -7290,6 +7735,7 @@ MinCED - Mining CRISPRs in Environmental Datasets + To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis @@ -7310,6 +7756,7 @@ Sequence assembly, Sequencing Polishing miniasm assemblies A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. + Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis @@ -7330,6 +7777,7 @@ Assembly mitogenomes from Pacbio HiFi read. + To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly @@ -7350,6 +7798,7 @@ converter + To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats @@ -7370,6 +7819,7 @@ Multi-subject Single Cell deconvolution (MuSiC) + Up-to-date https://github.com/xuranw/MuSiC Transcriptomics @@ -7390,6 +7840,7 @@ Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. + Up-to-date https://github.com/jts/nanopolish @@ -7410,6 +7861,7 @@ netboxr enables automated discovery of biological process modules by network analysis + To update Systems Biology @@ -7430,6 +7882,7 @@ Sequencing, Sequence assembly String graph-based de novo assembler for long reads NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. + To update https://github.com/Nextomics/NextDenovo Assembly @@ -7450,6 +7903,7 @@ Prediction of Nucleosomes Positions on the Genome + Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis @@ -7470,6 +7924,7 @@ Clustering tool for numberic values + To update http://scikit-learn.org/stable/index.html Statistics @@ -7490,6 +7945,7 @@ OpenMS in version 2.1. + To update Proteomics @@ -7510,6 +7966,7 @@ Rolling window calculations + To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics @@ -7530,6 +7987,7 @@ PEAKachu is a peak-caller for CLIP- and RIP-Seq data + To update Sequence Analysis, RNA @@ -7550,6 +8008,7 @@ suitable for boolean classification problems + To update http://osmot.cs.cornell.edu/kddcup/software.html @@ -7570,6 +8029,7 @@ Sequence analysis Search a FASTA sequence against a library of Pfam HMM. This tool is used to search a FASTA sequence against a library of Pfam HMM. + Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis @@ -7590,6 +8050,7 @@ tool suite for dealing with Postgresql databases from Galaxy's history + To update https://www.postgresql.org Data Export, Data Source @@ -7610,6 +8071,7 @@ Pharmacogenomics Clinical Annotation Tool + To update https://pharmcat.org/ Variant Analysis @@ -7630,6 +8092,7 @@ Piranha is a peak-caller for CLIP- and RIP-Seq data + To update Sequence Analysis, RNA @@ -7650,6 +8113,7 @@ efficient and accurate variant-detection in high-throughput sequencing data + To update http://www.well.ox.ac.uk/platypus Sequence Analysis @@ -7670,6 +8134,7 @@ performance plots for machine learning problems + To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization @@ -7690,6 +8155,7 @@ parallel coordinates plot produced with plotly + To update https://plot.ly/python/parallel-coordinates-plot/ Visualization @@ -7710,6 +8176,7 @@ performance plots for regression problems + To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization @@ -7730,6 +8197,7 @@ This tool can learn the cleavage specificity of a given class of proteases. + To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics @@ -7750,6 +8218,7 @@ Calculation of various properties from given protein sequences + To update Sequence Analysis @@ -7770,6 +8239,7 @@ Visualisation of PepXML files + To update http://www.improviser.uni-freiburg.de/ Proteomics @@ -7790,6 +8260,7 @@ Whole genome sequencing, Sequence assembly, Plant biology Consensus module for raw de novo DNA assembly of long uncorrected reads. The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads + Up-to-date https://github.com/isovic/racon Sequence Analysis @@ -7810,6 +8281,7 @@ RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. + To update http://www.repeatmasker.org/ Sequence Analysis @@ -7830,6 +8302,7 @@ A tool to replace all column entries of a file given by values of a key-value file. + To update Text Manipulation @@ -7850,6 +8323,7 @@ This tool fetches data from pubchem via the PubChem REST API. + To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source @@ -7870,6 +8344,7 @@ antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . + To update RNA @@ -7890,6 +8365,7 @@ AREsite2 REST Interface + To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis @@ -7910,6 +8386,7 @@ BlockClust detects transcripts with similar processing patterns. + Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA @@ -7930,6 +8407,7 @@ removes lower scoring overlaps from cmsearch results. + To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA @@ -7950,6 +8428,7 @@ cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. + Up-to-date https://github.com/eggzilla/cmv RNA @@ -7970,6 +8449,7 @@ Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. + To update http://www.e-rna.org/cofold/ RNA @@ -7990,6 +8470,7 @@ Compute fractional identity between trusted alignment and test alignment + Up-to-date RNA, Sequence Analysis @@ -8010,6 +8491,7 @@ Target prediction for prokaryotic trans-acting small RNAs + To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis @@ -8030,6 +8512,7 @@ DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data + To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq @@ -8050,6 +8533,7 @@ data source for RNA interactions in post-transcriptional regulation + To update RNA, Data Source @@ -8061,7 +8545,7 @@ dot2ct 5.7.a - 6.3 + 6.4 rnastructure To update @@ -8070,6 +8554,7 @@ Dot-Bracket to Connect Table (CT) + To update Sequence Analysis, RNA @@ -8090,6 +8575,7 @@ DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence + To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics @@ -8110,6 +8596,7 @@ ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. + Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA @@ -8130,6 +8617,7 @@ GraphProt models binding preferences of RNA-binding proteins. + To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq @@ -8150,6 +8638,7 @@ htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets + To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq @@ -8161,16 +8650,17 @@ infernal 1.1.4 - 1.1.4 + 1.1.5 infernal - Up-to-date + To update infernal Infernal Nucleic acid feature detection Sequence sites, features and motifs Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. - Up-to-date + + To update http://infernal.janelia.org/ RNA infernal @@ -8190,6 +8680,7 @@ INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. + To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA @@ -8210,6 +8701,7 @@ Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. + Up-to-date https://github.com/BackofenLab/IntaRNA RNA @@ -8230,6 +8722,7 @@ Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. + To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA @@ -8250,6 +8743,7 @@ LocARNA - A suite for multiple alignment and folding of RNAs + To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA @@ -8270,6 +8764,7 @@ Maximum expected accuracy prediction + To update http://www.bioinf.uni-leipzig.de/Software/mea RNA @@ -8290,6 +8785,7 @@ Ribosome profiling mapping quality control tool + To update https://github.com/Biobix/mQC Sequence Analysis @@ -8310,6 +8806,7 @@ A method to identify cis-NATs using ssRNA-seq + Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA @@ -8330,6 +8827,7 @@ A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. + Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA @@ -8350,6 +8848,7 @@ A method to identify novel plant miRNA. + To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA @@ -8370,6 +8869,7 @@ Identification of ribosomal RNA genes in metagenomic fragments. + To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA @@ -8390,6 +8890,7 @@ RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs + Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq @@ -8410,6 +8911,7 @@ RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments + To update https://github.com/BIMSBbioinfo/RCAS RNA @@ -8430,6 +8932,7 @@ Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. + Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA @@ -8450,6 +8953,7 @@ remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation + To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA @@ -8470,6 +8974,7 @@ Functional genomics A method for defining traslated ORFs using Ribosome Profiling data. New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. + To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA @@ -8490,6 +8995,7 @@ Compute secondary structures of RNA + To update RNA @@ -8510,6 +9016,7 @@ Fast pattern searching for RNA structural motifs + To update http://eddylab.org/software.html RNA @@ -8530,6 +9037,7 @@ Analyze the protein coding potential in MSA + To update RNA @@ -8550,6 +9058,7 @@ RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. + To update https://github.com/gianlucacorrado/RNAcommender RNA @@ -8570,6 +9079,7 @@ RNAlien unsupervized RNA family model construction + To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis @@ -8590,6 +9100,7 @@ RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs + To update http://rth.dk/resources/rnasnp/ RNA @@ -8610,6 +9121,7 @@ RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. + Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA @@ -8630,6 +9142,7 @@ SelectSequences - selects representative entries from a multiple sequence alignment in clustal format + Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis @@ -8650,6 +9163,7 @@ Metatranscriptomics, Metagenomics SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. + Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA @@ -8670,6 +9184,7 @@ ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data + Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA @@ -8690,6 +9205,7 @@ Plant small RNA target prediction tool + Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA @@ -8710,6 +9226,7 @@ Aragorn predicts tRNA and tmRNA in nucleotide sequences. + To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA @@ -8730,6 +9247,7 @@ ViennaRNA - Prediction and comparison of RNA secondary structures + To update http://www.tbi.univie.ac.at/RNA/ RNA @@ -8750,6 +9268,7 @@ Sailfish is a tool for transcript quantification from RNA-seq data + To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA @@ -8770,6 +9289,7 @@ Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. + To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics @@ -8790,6 +9310,7 @@ SAMBAMBA: process your BAM data faster! + To update https://github.com/lomereiter/sambamba SAM @@ -8810,6 +9331,7 @@ Manipulate your data with the sed command line tool. + To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation @@ -8830,6 +9352,7 @@ segemehl - short read mapping with gaps + To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers @@ -8850,6 +9373,7 @@ Machine Learning tool suite from Scikit-learn + To update http://scikit-learn.org Machine Learning, Statistics @@ -8870,6 +9394,7 @@ Split a multi-sequence fasta file into files containing single sequences + To update Text Manipulation @@ -8890,6 +9415,7 @@ Tool for computing statistical tests. + To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics @@ -8910,6 +9436,7 @@ stress test a computer system in various selectable ways + To update Web Services @@ -8917,6 +9444,27 @@ bgruening-util https://github.com/ColinIanKing/stress-ng + + + tapscan + 4.76+galaxy0 + 3.4 + hmmer + To update + + + + + Search for transcription associated proteins (TAPs) + + + To update + https://plantcode.cup.uni-freiburg.de/tapscan/ + Proteomics + tapscan + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/tapscan + add_line_to_file @@ -8930,6 +9478,7 @@ Adds a text line to the beginning or end of a file. + To update Text Manipulation @@ -8950,6 +9499,7 @@ Column arrange by header name + To update Text Manipulation @@ -8970,6 +9520,7 @@ Join two files on a common column, allowing a certain difference. + To update Text Manipulation @@ -8990,6 +9541,7 @@ Split a file on a specific column. + To update Text Manipulation @@ -9010,6 +9562,7 @@ Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. + To update Text Manipulation @@ -9020,7 +9573,7 @@ text_processing - 0.1.1 + 9.3 8.25 coreutils To update @@ -9030,6 +9583,7 @@ High performance text processing tools using the GNU coreutils, sed, awk and friends. + To update https://www.gnu.org/software/ Text Manipulation @@ -9050,6 +9604,7 @@ Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. + To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly @@ -9070,6 +9625,7 @@ Create model to recommend tools + To update https://github.com/bgruening/galaxytools Machine Learning @@ -9090,6 +9646,7 @@ Sequence analysis Trim Galore adaptive quality and adapter trimmer A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation @@ -9110,6 +9667,7 @@ UniProt ID mapping and sequence retrieval + To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis @@ -9130,6 +9688,7 @@ A tool set for short variant discovery in genetic sequence data. + To update Sequence Analysis, Variant Analysis @@ -9150,6 +9709,7 @@ Sequence assembly, Sequencing WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. + Up-to-date https://github.com/ruanjue/wtdbg2 Assembly @@ -9170,6 +9730,7 @@ Thread nucleotides onto a protein alignment (back-translation) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis @@ -9190,6 +9751,7 @@ Chromosome Diagrams using Biopython + To update Graphics, Sequence Analysis, Visualization @@ -9210,6 +9772,7 @@ Galaxy wrapper for the CLC Assembly Cell suite from CLCBio + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM @@ -9230,6 +9793,7 @@ NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins + To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis @@ -9250,6 +9814,7 @@ Count sequence variants in region of interest in BAM file + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM @@ -9270,6 +9835,7 @@ BAM coverage statistics using samtools idxstats and depth + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM @@ -9290,6 +9856,7 @@ Find bacterial type III effectors in protein sequences + To update http://effectors.org Sequence Analysis @@ -9310,6 +9877,7 @@ Filter FASTA sequences by ID (DEPRECATED) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation @@ -9330,6 +9898,7 @@ Filter FASTQ sequences by ID (DEPRECATED) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation @@ -9350,6 +9919,7 @@ Extract FASTQ paired read names + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis @@ -9370,6 +9940,7 @@ Divide FASTQ file into paired and unpaired reads + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation @@ -9390,6 +9961,7 @@ Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis @@ -9410,6 +9982,7 @@ Draw dotplots using mummer, mucmer, or promer with mummerplot + To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization @@ -9430,6 +10003,7 @@ Find nuclear localization signals (NLSs) in protein sequences + To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis @@ -9450,6 +10024,7 @@ Python reimplementation of predictNLS for Galaxy + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis @@ -9470,6 +10045,7 @@ TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis @@ -9490,6 +10066,7 @@ Sub-sample sequences files (e.g. to reduce coverage) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis @@ -9510,6 +10087,7 @@ Re-align a SAM/BAM file with a padded reference (using samtools depad) + To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis @@ -9530,6 +10108,7 @@ Coverage depth via samtools + To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM @@ -9550,6 +10129,7 @@ BAM mapping statistics (using samtools idxstats) + To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM @@ -9570,6 +10150,7 @@ Sequence composition + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis @@ -9590,6 +10171,7 @@ Filter sequences by ID + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation @@ -9610,6 +10192,7 @@ Filter sequencing reads using SAM/BAM mapping files + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis @@ -9630,6 +10213,7 @@ Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis @@ -9650,6 +10234,7 @@ Trim off 5' or 3' primers + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation @@ -9670,6 +10255,7 @@ Rename sequences with ID mapping from a tabular file + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation @@ -9690,6 +10276,7 @@ Select sequences by ID + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation @@ -9710,6 +10297,7 @@ Draw Venn Diagram (PDF) from lists, FASTA files, etc + To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization @@ -9730,6 +10318,7 @@ TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline + To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly @@ -9750,6 +10339,7 @@ Genomics, Microbiology Mass screening of contigs for antiobiotic resistance genes Mass screening of contigs for antimicrobial resistance or virulence genes. + Up-to-date https://github.com/tseemann/abricate Sequence Analysis @@ -9770,6 +10360,7 @@ A pipeline for running AMRfinderPlus and collating results into functional classes + Up-to-date https://zenodo.org/record/7370628 Sequence Analysis @@ -9780,17 +10371,18 @@ abyss - 2.3.6 + 2.3.7 2.3.7 abyss - To update + Up-to-date abyss ABySS Genome assembly, De-novo assembly, Scaffolding Sequence assembly Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler De novo genome sequence assembler using short reads. - To update + + Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss @@ -9810,6 +10402,7 @@ Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. + Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis @@ -9830,6 +10423,7 @@ Add input name as column on an existing tabular file + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation @@ -9850,6 +10444,7 @@ Sequence analysis, Gene structure AEGeAn toolkit wrappers Gene Annotation EVAluation. + Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis @@ -9870,6 +10465,7 @@ Gene expression, Statistics and probability Performs analysis Of differential abundance taking sample variation into account A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. + To update https://github.com/ggloor/ALDEx_bioc Metagenomics @@ -9890,6 +10486,7 @@ Sequence analysis, Transcription factors and regulatory sites, DNA Linkage and haplotype analysis from deCODE It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. + To update http://www.decode.com/software/ Variant Analysis @@ -9910,6 +10507,7 @@ PCR experiment, Statistics and probability AmpliCan is an analysis tool for genome editing. It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. + To update https://github.com/valenlab/amplican Sequence Analysis @@ -9920,7 +10518,7 @@ ampvis2 - 2.7.22 + 2.8.6 To update @@ -9930,6 +10528,7 @@ Biodiversity ampvis2 ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. + To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics @@ -9941,16 +10540,17 @@ amrfinderplus 3.11.26 - 3.11.26 + 3.12.8 ncbi-amrfinderplus - Up-to-date + To update amrfinderplus AMRFinderPlus Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms - Up-to-date + + To update https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus @@ -9970,6 +10570,7 @@ Microbial ecology, Metagenomics Performs analysis of compositions of microbiomes with bias correction. Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. + To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics @@ -9990,6 +10591,7 @@ Import, Export, Inspect and Manipulate Anndata and Loom objects + To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis @@ -10000,17 +10602,18 @@ annotatemyids - 3.17.0 + 3.18.0 3.18.0 bioconductor-org.hs.eg.db - To update + Up-to-date annotatemyids annotatemyids Annotation annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. - To update + + Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids @@ -10030,6 +10633,7 @@ Arriba detects fusion genes in RNA-Seq data after running RNA-STAR + Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics @@ -10050,6 +10654,7 @@ Bioinformatics Simulator for Illumina, 454, and SOLiD sequencing data ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD + To update Sequence Analysis, Data Source @@ -10070,6 +10675,7 @@ Genomics The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis @@ -10090,6 +10696,7 @@ Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. + Up-to-date https://github.com/rjchallis/assembly-stats Assembly @@ -10110,6 +10717,7 @@ Gene transcripts, Gene and protein families AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. + To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis @@ -10130,6 +10738,7 @@ This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA + To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology @@ -10140,17 +10749,18 @@ bakta - 1.8.2 + 1.9.2 1.9.2 bakta - To update + Up-to-date Bakta Bakta Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." Rapid & standardized annotation of bacterial genomes, MAGs & plasmids - To update + + Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta @@ -10170,6 +10780,7 @@ Contains a tool that converts a BAM file to an ScIdx file. + To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats @@ -10190,6 +10801,7 @@ bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. + To update https://github.com/statgen/bamUtil Sequence Analysis @@ -10210,6 +10822,7 @@ Genomics, Sequence assembly Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. + Up-to-date https://github.com/rrwick/Bandage Visualization @@ -10230,6 +10843,7 @@ A utility to split sequence files using multiple sets of barcodes + To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation @@ -10250,6 +10864,7 @@ RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. + Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization @@ -10270,6 +10885,7 @@ Genomics, Model organisms, Model organisms Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). + To update Sequence Analysis @@ -10290,6 +10906,7 @@ Breakpoint detection, including large insertions + Up-to-date https://github.com/seqan/anise_basil Variant Analysis @@ -10310,6 +10927,7 @@ BAX to BAM converter + Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis @@ -10330,6 +10948,7 @@ Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Detecting natural selection from population-based genetic data BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. + To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis @@ -10340,8 +10959,8 @@ bbtools - 39.01 - 39.01 + 39.06 + 39.06 bbmap Up-to-date @@ -10350,6 +10969,7 @@ BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. + Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis @@ -10370,6 +10990,7 @@ Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment BCFtools toolkit wrappers BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + To update https://samtools.github.io/bcftools/ Variant Analysis @@ -10390,6 +11011,7 @@ bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 + Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics @@ -10410,6 +11032,7 @@ beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). + Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis @@ -10430,6 +11053,7 @@ Beagle is a program for phasing and imputing missing genotypes. + To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis @@ -10450,6 +11074,7 @@ BEDOPS: high-performance genomic feature operations + Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations @@ -10470,6 +11095,7 @@ Genomics bedtools is a powerful toolset for genome arithmetic BEDTools is an extensive suite of utilities for comparing genomic features in BED format. + To update https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation @@ -10490,6 +11116,7 @@ Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. + Up-to-date https://github.com/davebx/bellerophon Sequence Analysis @@ -10510,6 +11137,7 @@ Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. + Up-to-date https://github.com/tseemann/berokka Fasta Manipulation @@ -10517,6 +11145,27 @@ iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka + + + bigscape + 1.1.9 + 1.1.9 + bigscape + Up-to-date + + + + + Construct sequence similarity networks of BGCs and groups them into GCF + + + Up-to-date + https://github.com/medema-group/BiG-SCAPE + Metagenomics + bigscape + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ + binning_refiner @@ -10530,6 +11179,7 @@ Metagenomics Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. Improving genome bins through the combination of different binning programs + Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics @@ -10540,17 +11190,18 @@ bioext - 0.20.4 + 0.21.2 0.21.2 python-bioext - To update + Up-to-date A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! - To update + + Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers @@ -10570,6 +11221,7 @@ Miscellanea of scripts for bioinformatics + To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis @@ -10584,11 +11236,12 @@ 2.1.7 biom-format To update - - - - + biomformat + biomformat + Formatting + Laboratory information management, Sequence analysis The biom-format package provides a command line interface and Python API for working with BIOM files. + This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. To update https://github.com/biocore/biom-format @@ -10610,6 +11263,7 @@ Genomics, Software engineering, Data management Converts GenBank format files to GFF3 A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. + To update https://bioperl.org/ Sequence Analysis @@ -10630,6 +11284,7 @@ Bionano scaffolding correction tool + Up-to-date https://github.com/institut-de-genomique/biscot Assembly @@ -10650,6 +11305,7 @@ Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome + Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers @@ -10670,6 +11326,7 @@ BlastXML to gapped GFF3 + To update Convert Formats, Sequence Analysis @@ -10680,17 +11337,18 @@ bowtie2 - 2.5.0 + 2.5.3 2.5.3 bowtie2 - To update + Up-to-date bowtie2 Bowtie 2 Read mapping Mapping, Genomics, Mapping Bowtie2: Fast and sensitive read alignment Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. - To update + + Up-to-date http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 @@ -10710,6 +11368,7 @@ Metagenomics, Microbial ecology Bayesian Reestimation of Abundance with KrakEN Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics @@ -10721,7 +11380,7 @@ breseq 0.35.5 - 0.38.2 + 0.38.3 breseq To update breseq @@ -10730,6 +11389,7 @@ Sequencing, Sequence analysis, DNA mutation Predicts mutations in microbial genomes Runs Breseq software on a set of fastq files. + To update https://github.com/barricklab/breseq Variant Analysis @@ -10750,6 +11410,7 @@ Sequence assembly, Genomics, Transcriptomics, Sequence analysis BUSCO assess genome and annotation completeness Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis @@ -10770,6 +11431,7 @@ Mapping Wrapper for bwa mem, aln, sampe, and samse Fast, accurate, memory-efficient aligner for short and long sequencing reads + Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers @@ -10790,6 +11452,7 @@ Mapping Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. + Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers @@ -10810,6 +11473,7 @@ Fast and accurate alignment of BS-seq reads + To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers @@ -10819,16 +11483,38 @@ - calculate_contrast_threshold - 1.0.0 - - numpy - To update - + cactus + 2.7.1 + To update + cactus + Cactus + Multiple sequence alignment, Genome alignment + Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics + Cactus is a reference-free whole-genome multiple alignment program + Cactus is a reference-free whole-genome multiple alignment program. + + To update + https://github.com/ComparativeGenomicsToolkit/cactus + Sequence Analysis + cactus + galaxy-australia + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus + + + + calculate_contrast_threshold + 1.0.0 + + numpy + To update + + + + + Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. - Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold @@ -10850,6 +11536,7 @@ Calculate a numeric parameter value using integer and float values. + To update Text Manipulation @@ -10864,11 +11551,12 @@ 5.3 cat To update - - - - + cat_bins + CAT and BAT + Taxonomic classification, Sequence assembly, Coding region prediction + Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Contig Annotation Tool (CAT) + Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. To update https://github.com/dutilh/CAT @@ -10890,6 +11578,7 @@ Sequencing Cluster or compare biological sequence datasets Cluster a nucleotide dataset into representative sequences. + Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation @@ -10910,6 +11599,7 @@ Gene expression, Transcriptomics, Microarray experiment Gene co-expression network analysis tool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics @@ -10930,6 +11620,7 @@ Enables advanced visualization options in Galaxy Charts + To update Visualization @@ -10950,6 +11641,7 @@ Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + To update https://github.com/Ecogenomics/CheckM Metagenomics @@ -10967,9 +11659,10 @@ cherri cherri - + Molecular interactions, pathways and networks, Structure analysis, Machine learning Computational Help Evaluating RNA-RNA interactions CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. + To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA @@ -10990,6 +11683,7 @@ RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Chimeric Read Annotator for RNA-RNA interactome data ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. + Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis @@ -11010,6 +11704,7 @@ Domain-Agnostic Supervised Learning with Hyperdimensional Computing + To update https://github.com/cumbof/chopin2 Machine Learning @@ -11030,6 +11725,7 @@ ultra-fast pairwise genome comparisons + Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis @@ -11050,6 +11746,7 @@ RNA splicing, Gene transcripts, Literature and language Comprehensive and integrative circular RNA analysis toolset. Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. + Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly @@ -11070,6 +11767,7 @@ Build Circos Plots in Galaxy Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. + To update http://circos.ca/ Graphics @@ -11090,6 +11788,7 @@ Transcriptomics, Immunoproteins and antigens Count CMO/HTO Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. + Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics @@ -11110,6 +11809,7 @@ Molecular genetics Symphonizing pileup and full-alignment for high-performance long-read variant calling Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. + To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis @@ -11130,6 +11830,7 @@ ClustalW multiple sequence alignment program for DNA or proteins + Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis @@ -11137,6 +11838,48 @@ devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw + + + cnv-phenopacket + 1.0.2 + + cnv-phenopacket + To update + + + + + cnv-phenopacket Converts TSV metadata file to JSON. + + + To update + https://pypi.org/project/cnv-phenopacket/ + Variant Analysis + cnv_phenopacket + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket + + + + cnv-vcf2json + 1.0.4 + + cnv-vcf2json + To update + + + + + cnv-vcf2json Converts structural variants VCF file to JSON. + + + To update + https://pypi.org/project/cnv-phenopacket/ + Variant Analysis + cnv-vcf2json + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json + cnvkit @@ -11150,6 +11893,7 @@ DNA structural variation detecting copy number variants and alterations genome-wide from high-throughput sequencing CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. + Up-to-date https://github.com/etal/cnvkit Variant Analysis @@ -11164,11 +11908,12 @@ 4.10.7 paml To update - - - - + paml + PAML + Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis + Phylogenetics, Sequence analysis Detects positive selection + Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. To update http://abacus.gene.ucl.ac.uk/software/paml.html @@ -11190,6 +11935,7 @@ Genetic variation co-occurrence of mutations on amplicons CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. + Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis @@ -11210,6 +11956,7 @@ Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome + To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis @@ -11230,6 +11977,7 @@ Column Join on Collections + To update Text Manipulation @@ -11250,6 +11998,7 @@ Extract element identifiers of a collection + To update Text Manipulation @@ -11270,6 +12019,7 @@ Compute an expression on every row + To update Text Manipulation @@ -11290,6 +12040,7 @@ Sort Column Order by heading + To update Text Manipulation @@ -11310,6 +12061,7 @@ Remove columns by header + To update Text Manipulation @@ -11317,6 +12069,27 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header + + + compleasm + 0.2.5 + 0.2.5 + compleasm + Up-to-date + + + + + Compleasm: a faster and more accurate reimplementation of BUSCO + + + Up-to-date + https://github.com/huangnengCSU/compleasm + Sequence Analysis + compleasm + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ + compose_text_param @@ -11330,6 +12103,7 @@ Compose a text parameter value using text, integer and float values + To update Text Manipulation @@ -11350,6 +12124,7 @@ Compress files. + To update Text Manipulation @@ -11370,6 +12145,7 @@ Metagenomics CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. + Up-to-date https://github.com/BinPro/CONCOCT Metagenomics @@ -11390,6 +12166,7 @@ Generate Detailed Coverage Report from BAM file + To update https://github.com/galaxyproject/tools-iuc Sequence Analysis @@ -11400,17 +12177,18 @@ coverm - 0.6.1 + 0.7.0 0.7.0 coverm - To update + Up-to-date coverm CoverM Local alignment Bioinformatics CoverM genome and contig wrappers Read coverage calculator for metagenomics - To update + + Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm @@ -11430,6 +12208,7 @@ CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. + To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis @@ -11450,6 +12229,7 @@ Barcode contamination discovery tool + To update Transcriptomics, Visualization @@ -11470,6 +12250,7 @@ CrossMap converts genome coordinates or annotation files between genome assemblies + To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations @@ -11490,6 +12271,7 @@ Genomics, Probes and primers, Sequencing Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. + Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis @@ -11510,6 +12292,7 @@ DNA structural variation, Sequencing, Computer science Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis + To update https://github.com/tjiangHIT/cuteSV Variant Analysis @@ -11530,6 +12313,7 @@ Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. + To update ChIP-seq @@ -11550,6 +12334,7 @@ Sequencing, Genetic variation, Microbial ecology, Metagenomics DADA2 wrappers This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. + To update https://benjjneb.github.io/dada2/index.html Metagenomics @@ -11560,17 +12345,18 @@ das_tool - 1.1.6 + 1.1.7 1.1.7 das_tool - To update + Up-to-date dastool dastool Read binning Metagenomics DAS Tool for genome resolved metagenomics DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. - To update + + Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool @@ -11590,6 +12376,7 @@ IRIS-TCGA Data source tool + To update Data Source @@ -11610,6 +12397,7 @@ GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. + To update https://www.gnu.org/software/datamash/ Text Manipulation @@ -11630,6 +12418,7 @@ Deep Learning method for novel virus detection in sequencing data + To update https://github.com/cbib/decontaminator Machine Learning @@ -11650,6 +12439,7 @@ Representation learning and classification framework + Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning @@ -11670,6 +12460,7 @@ Predictor of signal peptides in proteins based on deep learning + Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation @@ -11690,6 +12481,7 @@ DeepVariant is a deep learning-based variant caller + To update https://github.com/google/deepvariant Variant Analysis @@ -11710,6 +12502,7 @@ Annotate DESeq2/DEXSeq output tables + To update Transcriptomics @@ -11730,6 +12523,7 @@ DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. + To update https://github.com/dellytools/delly Variant Analysis @@ -11750,6 +12544,7 @@ Transcriptomics Differential gene expression analysis based on the negative binomial distribution R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics @@ -11770,6 +12565,7 @@ RNA-Seq Inference of differential exon usage in RNA-Seq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. + To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics @@ -11781,7 +12577,7 @@ diamond 2.0.15 - 2.1.8 + 2.1.9 diamond To update diamond @@ -11790,6 +12586,7 @@ Sequence analysis, Proteins DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. + To update https://github.com/bbuchfink/diamond Sequence Analysis @@ -11810,6 +12607,7 @@ ChIP-seq Diffbind provides functions for processing ChIP-Seq data. Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq @@ -11820,8 +12618,8 @@ dimet - 0.1.4 0.2.1 + 0.2.2 dimet To update @@ -11830,6 +12628,7 @@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. + To update https://github.com/cbib/DIMet Metabolomics @@ -11850,6 +12649,7 @@ Structure determination DISCO is a overlap-layout-consensus (OLC) metagenome assembler DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. + To update http://disco.omicsbio.org/ Metagenomics, Assembly @@ -11870,6 +12670,7 @@ DNA assembly using BASIC on OpenTrons + To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology @@ -11890,6 +12691,7 @@ Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. + Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology @@ -11904,11 +12706,12 @@ 1.4.6 dram To update - - - - + dram + DRAM + Gene functional annotation + Metagenomics, Biological databases, Molecular genetics DRAM for distilling microbial metabolism to automate the curation of microbiome function + Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes To update https://github.com/WrightonLabCSU/DRAM @@ -11921,16 +12724,17 @@ drep 3.4.5 - 3.4.5 + 3.5.0 drep - Up-to-date + To update drep dRep Genome comparison Metagenomics, Genomics, Sequence analysis dRep compares and dereplicates genome sets Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. - Up-to-date + + To update https://github.com/MrOlm/drep Metagenomics drep @@ -11950,6 +12754,7 @@ Gene expression, RNA-seq, Sequencing, Transcriptomics DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. + To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis @@ -11970,6 +12775,7 @@ Tools to query and download data from several EMBL-EBI databases + To update http://www.ebi.ac.uk/services/all Web Services, Data Source @@ -11990,6 +12796,7 @@ Genetics, RNA-Seq, ChIP-seq Perform RNA-Seq differential expression analysis using edgeR pipeline Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics @@ -12010,6 +12817,7 @@ Systems biology This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. + To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics @@ -12030,6 +12838,7 @@ Molecular biology, Sequence analysis, Biology Galaxy wrappers for EMBOSS version 5.0.0 tools Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. + To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation @@ -12041,7 +12850,7 @@ ena_upload 0.6.3 - 0.7.0 + 0.7.1 ena-upload-cli To update @@ -12050,6 +12859,7 @@ Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). + To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export @@ -12070,6 +12880,7 @@ A Python library for interacting with ENA's API + To update https://github.com/bebatut/enasearch Data Source @@ -12090,6 +12901,7 @@ Ensembl VEP: Annotate VCFs with variant effect predictions + To update https://github.com/Ensembl/ensembl-vep Variant Analysis @@ -12110,6 +12922,7 @@ Epigenomics, Cell biology, DNA EpiScanpy – Epigenomics single cell analysis in python Epigenomics Single Cell Analysis in Python. + To update https://github.com/colomemaria/epiScanpy Epigenetics @@ -12130,6 +12943,7 @@ Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. + To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis @@ -12150,6 +12964,7 @@ Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Exonerate is a generic tool for pairwise sequence comparison. A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. + Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis @@ -12164,11 +12979,12 @@ 0.22 export2graphlan To update - - - - + export2graphlan + export2graphlan + Conversion + Taxonomy, Metabolomics, Biomarkers export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn + export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. To update https://bitbucket.org/CibioCM/export2graphlan/overview @@ -12181,7 +12997,7 @@ extract_genomic_dna 3.0.3+galaxy2 - 0.10.0 + 0.11.0 bx-python To update @@ -12190,6 +13006,7 @@ Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. + To update Genomic Interval Operations @@ -12204,11 +13021,12 @@ 0.1 fargene Up-to-date - - - - + fargene + fARGene + Antimicrobial resistance prediction + Metagenomics, Microbiology, Public health and epidemiology fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Up-to-date https://github.com/fannyhb/fargene @@ -12230,6 +13048,7 @@ Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. + To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization @@ -12250,6 +13069,7 @@ Display summary statistics for a fasta file. + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis @@ -12270,6 +13090,7 @@ Fast alignment-free computation of whole-genome Average Nucleotide Identity + To update https://github.com/ParBLiSS/FastANI Sequence Analysis @@ -12290,6 +13111,7 @@ Fast all-in-one preprocessing for FASTQ files + To update https://github.com/OpenGene/fastp Sequence Analysis @@ -12310,6 +13132,7 @@ Sequencing, Data quality management, Sequence analysis Read QC reports using FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. + To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation @@ -12324,14 +13147,15 @@ 0.3.1 fastqe To update - - - - + fastqe + FASTQE + Sequencing quality control + Sequence analysis, Sequencing FASTQE + Compute quality stats for FASTQ files and print those stats as emoji... for some reason. To update - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe + https://fastqe.com/ Sequence Analysis fastqe iuc @@ -12350,6 +13174,7 @@ Phylogenetics, Sequence analysis FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. + To update http://www.microbesonline.org/fasttree/ Phylogenetics @@ -12370,6 +13195,7 @@ Sequencing featureCounts counts the number of reads aligned to defined masked regions in a reference genome featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. + To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis @@ -12390,6 +13216,7 @@ RNA-seq, Functional, regulatory and non-coding RNA Galaxy wrapper for FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. + To update https://github.com/tderrien/FEELnc Sequence Analysis @@ -12410,6 +13237,7 @@ FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. + Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis @@ -12430,6 +13258,7 @@ Genetics Perform gene set testing using fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. + To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics @@ -12450,6 +13279,7 @@ Filtlong - Filtering long reads by quality + Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis @@ -12470,6 +13300,7 @@ FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. + To update https://github.com/BrooksLabUCSC/flair Nanopore @@ -12490,6 +13321,7 @@ Sequencing, Sequence assembly Fast Length Adjustment of SHort reads Identifies paired-end reads which overlap in the middle, converting them to single long reads + Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation @@ -12510,6 +13342,7 @@ Genetics, Sequence analysis Tool for finding (fragmented) genes in short read Application for finding (fragmented) genes in short reads + To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis @@ -12530,6 +13363,7 @@ Genomics, Genetic variation, Rare diseases Galaxy Freebayes Bayesian genetic variant detector tool Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. + To update https://github.com/ekg/freebayes Variant Analysis @@ -12550,6 +13384,7 @@ DNA structural variation, Oncology, Human genetics, Data mining Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. + To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis @@ -12561,7 +13396,7 @@ freyja 1.4.4 - 1.4.8 + 1.4.9 freyja To update freyja @@ -12570,6 +13405,7 @@ lineage abundances estimation + To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis @@ -12590,6 +13426,7 @@ Tool that plots a histogram of sizes of read families + To update Graphics @@ -12610,6 +13447,7 @@ Funannotate is a genome prediction, annotation, and comparison software package. + To update https://funannotate.readthedocs.io Genome annotation @@ -12621,7 +13459,7 @@ gatk4 4.1.7.0 - 4.4.0.0 + 4.5.0.0 gatk4 To update @@ -12630,6 +13468,7 @@ A Galaxy wrapper for Mutect2 from GATK + To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis @@ -12650,6 +13489,7 @@ GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format + To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats @@ -12670,6 +13510,7 @@ Ungapped genome comparison + Up-to-date https://github.com/otorreno/gecko Sequence Analysis @@ -12690,6 +13531,7 @@ Sequence analysis GEMINI: a flexible framework for exploring genome variation GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. + To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers @@ -12710,6 +13552,7 @@ Stitch gene blocks given a set of coding exon intervals + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations @@ -12730,6 +13573,7 @@ Maximised LOD score pedigree analysis utility + To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis @@ -12750,6 +13594,7 @@ Gene.iobio is an interactive tool for variant and trio analysis. + To update https://github.com/iobio/gene.iobio Sequence Analysis @@ -12770,6 +13615,7 @@ Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. + To update ChIP-seq @@ -12790,6 +13636,7 @@ Analyze unassembled short reads + Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics @@ -12810,6 +13657,7 @@ RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment Interpretation of RNAseq experiments through robust, efficient comparison to public databases GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. + To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics @@ -12830,6 +13678,7 @@ Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). + To update https://github.com/jsh58/Genrich ChIP-seq @@ -12850,6 +13699,7 @@ Annotate indel variants with homopolymer context + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis @@ -12870,6 +13720,7 @@ Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. + Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly @@ -12890,6 +13741,7 @@ gfa_to_fa - Converting GFA format to Fasta format + To update http://gfa-spec.github.io/GFA-spec/ Convert Formats @@ -12910,6 +13762,7 @@ Rebase a GFF against a parent GFF (e.g. an original genome) + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis @@ -12930,6 +13783,7 @@ Nucleic acids, Sequence analysis Galaxy wrappers for Geo Pertea's GffCompare package. Program for comparing, annotating, merging and tracking transcripts in GFF files. + Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics @@ -12950,6 +13804,7 @@ Nucleic acids, Sequence analysis gffread filters and/or converts GFF3/GTF2 records program for filtering, converting and manipulating GFF files + Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis @@ -12970,6 +13825,7 @@ Data visualisation ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. Plotting system for R, based on the grammar of graphics. + To update https://github.com/tidyverse/ggplot2 Visualization @@ -12990,6 +13846,7 @@ Create Upset Plots with ggupset + To update https://github.com/const-ae/ggupset Graphics @@ -13010,6 +13867,7 @@ Sequence analysis Glimmer makes gene predictions. GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. + To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis @@ -13030,6 +13888,7 @@ Transcriptomics Performs GO Enrichment analysis. GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. + Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation @@ -13050,6 +13909,7 @@ RNA-Seq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis @@ -13070,6 +13930,7 @@ functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more + To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services @@ -13090,6 +13951,7 @@ Compute a 2D embedding of a data matrix given supervised class information + Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics @@ -13104,14 +13966,15 @@ 1.1.3 graphlan To update - - - - + graphlan + GraPhlAn + Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification + Metagenomics, Phylogenetics, Phylogenomics, Cladistics GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees + GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. To update - https://bitbucket.org/nsegata/graphlan/overview + https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc @@ -13120,17 +13983,18 @@ gtdbtk - 2.2.2 + 2.3.2 2.3.2 gtdbtk - To update - - - - + Up-to-date + GTDB-Tk + GTDB-Tk + Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval + Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. + a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). - To update + Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk @@ -13150,6 +14014,7 @@ Sequence analysis Convert GTF files to BED12 format Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats @@ -13161,7 +14026,7 @@ gubbins 3.2.1 - 3.3.1 + 3.3.3 gubbins To update gubbins @@ -13170,6 +14035,7 @@ Phylogeny, Genotype and phenotype, Whole genome sequencing Gubbins - bacterial recombination detection Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. + To update Sequence Analysis @@ -13190,6 +14056,7 @@ + To update https://github.com/sequencing/gvcftools Variant Analysis @@ -13210,6 +14077,7 @@ GWAS study Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. + To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis @@ -13224,11 +14092,12 @@ 1.1.4 hamronization To update - - - - + hamronization + hAMRonization + Data handling, Antimicrobial resistance prediction, Parsing + Public health and epidemiology, Microbiology, Bioinformatics Convert AMR gene detection tool output to hAMRonization specification format. + Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure To update https://github.com/pha4ge/hAMRonization @@ -13250,6 +14119,7 @@ Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Heidelberg and Enteritidis SNP Elucidation BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. + Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis @@ -13270,6 +14140,7 @@ Robust and accurate haplotype assembly for diverse sequencing technologies HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md + Up-to-date https://github.com/vibansal/HapCUT2 Assembly @@ -13280,17 +14151,18 @@ hapog - 1.3.6 + 1.3.7 1.3.7 hapog - To update - - - - + Up-to-date + hapog + Hapo-G + Genome assembly, Optimisation and refinement + Sequence assembly, Genomics Hapo-G - Haplotype-Aware Polishing of Genomes + Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. - To update + Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog @@ -13310,6 +14182,7 @@ Genomics, DNA polymorphism A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. + To update https://github.com/Illumina/hap.py Variant Analysis @@ -13320,7 +14193,7 @@ heatmap2 - 3.1.3 + 3.1.3.1 2.17.0 r-gplots To update @@ -13330,6 +14203,7 @@ heatmap.2 function from the R gplots package + To update https://github.com/cran/gplots Visualization @@ -13350,6 +14224,7 @@ Molecular interactions, pathways and networks, Protein interactions An algorithm for identification of the optimal scoring subnetwork. This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. + To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics @@ -13370,6 +14245,7 @@ HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. + To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization @@ -13381,7 +14257,7 @@ hicstuff 3.1.5 - 3.2.1 + 3.2.2 hicstuff To update @@ -13390,6 +14266,7 @@ + To update https://github.com/koszullab/hicstuff Sequence Analysis @@ -13404,11 +14281,12 @@ hamtv0.3.1 hifiasm_meta To update - - - - + hifiasm-meta + Hifiasm-meta + Sequence assembly + Sequence assembly, Metagenomics A hifiasm fork for metagenome assembly using Hifi reads. + Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta @@ -13430,6 +14308,7 @@ RNA-seq HISAT2 is a fast and sensitive spliced alignment program. Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). + Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly @@ -13450,6 +14329,7 @@ Infers transmission networks from pairwise distances inferred by tn93 + To update https://pypi.org/project/hivclustering/ Next Gen Mappers @@ -13460,17 +14340,18 @@ hmmer3 - 3.3.2 + 3.4 3.4 hmmer - To update + Up-to-date hmmer3 HMMER3 Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. - To update + + Up-to-date http://hmmer.org/ Sequence Analysis @@ -13490,6 +14371,7 @@ HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. + Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis @@ -13500,17 +14382,18 @@ htseq_count - 0.9.1+galaxy1 + 2.0.5 2.0.5 htseq - To update + Up-to-date htseq HTSeq Nucleic acid sequence analysis Sequence analysis Count aligned reads (SAM/BAM) that overlap genomic features (GFF) Python framework to process and analyse high-throughput sequencing (HTS) data - To update + + Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count @@ -13530,6 +14413,7 @@ Metagenomics, Phylogenomics HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” + Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics @@ -13550,6 +14434,7 @@ Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Analyse targeted sequence capture data Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. + Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics @@ -13570,6 +14455,7 @@ Phylogeny, Small molecules, Molecular interactions, pathways and networks Hypothesis Testing using Phylogenies Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. + To update http://www.hyphy.org Phylogenetics @@ -13590,6 +14476,7 @@ Sequence assembly, Genomics Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. + Up-to-date https://github.com/kensung-lab/hypo Assembly @@ -13601,16 +14488,17 @@ icescreen 1.3.1 - 1.3.1 + 1.3.2 icescreen - Up-to-date - - - - + To update + icescreen + ICEscreen + Database search, Protein feature detection + Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. + A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. - Up-to-date + To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen @@ -13630,6 +14518,7 @@ Sequence assembly Wrappers for the idba assembler variants. A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. + To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly @@ -13650,6 +14539,7 @@ Galaxy wrappers for the IDR package from Nathan Boleu + To update https://github.com/nboley/idr Sequence Analysis @@ -13670,6 +14560,7 @@ Image Data Resource downloading tool + To update https://idr.openmicroscopy.org Data Source @@ -13690,6 +14581,7 @@ Get epitope binding predictions from IEDB-API + To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis @@ -13710,6 +14602,7 @@ Mapping, Metagenomics InStrain is a tool for analysis of co-occurring genome populations from metagenomes InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification + To update https://instrain.readthedocs.io/en/latest/# Metagenomics @@ -13720,17 +14613,18 @@ integron_finder - 2.0.2 - 3.4 - hmmer - To update + 2.0.3 + 2.0.3 + integron_finder + Up-to-date integron_finder Integron Finder Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" A tool to detect Integron in DNA sequences. - To update + + Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder @@ -13750,6 +14644,7 @@ InterMine Exporter + To update Convert Formats @@ -13761,7 +14656,7 @@ interproscan 5.59-91.0 - 5.59_91.0 + interproscan To update interproscan_ebi @@ -13770,6 +14665,7 @@ Gene and protein families, Sequence analysis Interproscan queries the interpro database and provides annotations. Scan sequences against the InterPro protein signature databases. + To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis @@ -13781,7 +14677,7 @@ interval2maf 1.0.1+galaxy1 - 0.10.0 + 0.11.0 bx-python To update bx-python @@ -13790,6 +14686,7 @@ Sequence analysis Extract MAF blocks given a set of intervals Tools for manipulating biological data, particularly multiple sequence alignments. + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations @@ -13810,6 +14707,7 @@ Computational biology Create pairwise and upset plots Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. + Up-to-date https://intervene.readthedocs.io Statistics @@ -13830,6 +14728,7 @@ Efficient phylogenomic software by maximum likelihood + To update http://www.iqtree.org/ Phylogenetics @@ -13850,6 +14749,7 @@ Refine insertion sequences + To update https://github.com/mkirsche/Iris Variant Analysis @@ -13870,6 +14770,7 @@ Genomics, DNA structural variation, Sequence analysis, Genetic variation "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." Automated identification of insertion sequence elements in prokaryotic genomes. + To update https://github.com/xiezhq/ISEScan Sequence Analysis @@ -13890,6 +14791,7 @@ Computational biology, Gene transcripts Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. + To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics @@ -13910,6 +14812,7 @@ iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing + Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis @@ -13930,6 +14833,7 @@ Statistics and probability Interval-Wise Testing for Omics Data Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. + To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics @@ -13950,6 +14854,7 @@ Merge structural variants across samples + To update https://github.com/mkirsche/Jasmine/ Variant Analysis @@ -13970,6 +14875,7 @@ Genomics JBrowse Genome Browser integrated as a Galaxy Tool Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. + Up-to-date https://jbrowse.org Sequence Analysis @@ -13990,6 +14896,7 @@ Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) + To update https://github.com/tanghaibao/jcvi Sequence Analysis @@ -14001,7 +14908,7 @@ jellyfish - 2.3.0 + 2.3.1 kmer-jellyfish To update Jellyfish @@ -14010,6 +14917,7 @@ Sequence analysis, Genomics Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA A command-line algorithm for counting k-mers in DNA sequence. + To update https://github.com/gmarcais/Jellyfish Assembly @@ -14030,6 +14938,7 @@ This tool will join datasets according to a column with identifier + To update Text Manipulation @@ -14050,6 +14959,7 @@ JQ is a lightweight and flexible command-line JSON processor + To update https://stedolan.github.io/jq/ Text Manipulation @@ -14070,6 +14980,7 @@ Jvarkit : Java utilities for Bioinformatics + Up-to-date https://lindenb.github.io/jvarkit/ SAM @@ -14090,6 +15001,7 @@ Transcriptomics, RNA-seq, Gene expression kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. + To update https://pachterlab.github.io/kallisto/ Transcriptomics @@ -14110,6 +15022,7 @@ Mapping Kc-Align custom tool A fast and accurate tool for performing codon-aware multiple sequence alignments + Up-to-date https://github.com/davebx/kc-align Sequence Analysis @@ -14130,6 +15043,7 @@ Sequence assembly In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. + Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers @@ -14150,6 +15064,7 @@ Kinship-based INference for Gwas + Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis @@ -14170,6 +15085,7 @@ Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). + Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics @@ -14181,7 +15097,7 @@ kma 1.2.21 - 1.4.9 + 1.4.14 kma To update @@ -14190,6 +15106,7 @@ Map with KMA + To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers @@ -14210,6 +15127,7 @@ Gene function annotation tool based on KEGG Orthology and hidden Markov model + Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis @@ -14230,6 +15148,7 @@ Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) + Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics @@ -14250,6 +15169,7 @@ Kraken taxonomy report + To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics @@ -14270,6 +15190,7 @@ Taxonomy, Metagenomics KrakenTools is a suite of scripts to be used alongside the Kraken KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files + Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics @@ -14290,6 +15211,7 @@ Predict MLST directly from uncorrected long reads + To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis @@ -14301,7 +15223,7 @@ last 1205 - 1526 + 1542 last To update last @@ -14310,6 +15232,7 @@ Genomics, Comparative genomics LAST finds similar regions between sequences. Short read alignment program incorporating quality scores + To update http://last.cbrc.jp/ Sequence Analysis @@ -14330,6 +15253,7 @@ Genomics Galaxy wrappers for the Lastz and Lastz_d A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. + Up-to-date https://github.com/lastz/lastz Next Gen Mappers @@ -14350,6 +15274,7 @@ Ligase Chain Reaction Genie + To update https://github.com/neilswainston/LCRGenie Synthetic Biology @@ -14370,6 +15295,7 @@ Performs in silico Legionella pneumophila sequence based typing. + Up-to-date https://github.com/tseemann/legsta Sequence Analysis @@ -14390,6 +15316,7 @@ Gets gene length and gc content from a fasta and a GTF file + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis @@ -14400,17 +15327,18 @@ limma_voom - 3.50.1 + 3.58.1 3.58.1 bioconductor-limma - To update + Up-to-date limma limma RNA-Seq analysis Molecular biology, Genetics Perform RNA-Seq differential expression analysis using limma voom pipeline Data analysis, linear models and differential expression for microarray data. - To update + + Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom @@ -14420,7 +15348,7 @@ lineagespot - 1.4.0 + 1.6.0 r-base To update @@ -14430,6 +15358,7 @@ Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). + To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis @@ -14450,6 +15379,7 @@ Sequence assembly, Mapping, Sequencing Scaffold genome assemblies with long reads. LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. + Up-to-date https://github.com/bcgsc/LINKS Assembly @@ -14470,6 +15400,7 @@ LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. + Up-to-date https://csb5.github.io/lofreq/ Variant Analysis @@ -14490,6 +15421,7 @@ Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis @@ -14510,6 +15442,7 @@ LUMPY - a general probabilistic framework for structural variant discovery + Up-to-date http://layerlab.org/software/ Variant Analysis @@ -14530,6 +15463,7 @@ RNA-Seq, Transcriptomics, RNA, Machine learning m6anet to detect m6A RNA modifications from nanopore data Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. + Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis @@ -14550,6 +15484,7 @@ MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. + Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics @@ -14570,6 +15505,7 @@ ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites MACS - Model-based Analysis of ChIP-Seq Model-based Analysis of ChIP-seq data. + Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics @@ -14590,6 +15526,7 @@ MAF Coverage statistics + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations @@ -14610,6 +15547,7 @@ Genetics, Genetic variation, Genomics Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. + To update https://sourceforge.net/projects/mageck/ Genome editing @@ -14630,6 +15568,7 @@ Genomics, DNA, Sequence analysis MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. + To update http://www.yandell-lab.org/software/maker.html Sequence Analysis @@ -14641,7 +15580,7 @@ malt 0.5.3 - 0.61 + 0.62 malt To update @@ -14650,6 +15589,7 @@ Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. + To update https://github.com/husonlab/malt Next Gen Mappers @@ -14670,6 +15610,7 @@ Map a parameter value to another value + To update Text Manipulation @@ -14690,6 +15631,7 @@ fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. + To update https://github.com/jfmrod/MAPseq Metagenomics @@ -14710,6 +15652,7 @@ Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Fast genome and metagenome distance estimation using MinHash Fast genome and metagenome distance estimation using MinHash. + Up-to-date https://github.com/marbl/Mash Metagenomics @@ -14717,6 +15660,27 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash + + + mashmap + 3.1.3 + 3.1.3 + mashmap + Up-to-date + + + + + Fast local alignment boundaries + + + Up-to-date + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap + Sequence Analysis + mashmap + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap + masigpro @@ -14730,6 +15694,7 @@ Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Identify significantly differential expression profiles in time-course microarray experiments Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. + To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics @@ -14750,6 +15715,7 @@ Metagenomics, Sequence assembly, Microbiology clusters metagenomic contigs into bins Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. + To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics @@ -14770,6 +15736,7 @@ Molecular interactions, pathways and networks The Markov Cluster Algorithm, a cluster algorithm for graphs MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. + Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis @@ -14790,6 +15757,7 @@ Sequence assembly, Machine learning Sequence correction provided by ONT Research medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. + To update https://github.com/nanoporetech/medaka Sequence Analysis @@ -14810,6 +15778,7 @@ Metagenomics, Sequencing, Ecology, Sequence assembly An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. + Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics @@ -14830,6 +15799,7 @@ Metagenomics, Sequencing, Ecology, Sequence assembly A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. + To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics @@ -14841,7 +15811,7 @@ megan 6.21.7 - 6.24.20 + 6.25.9 megan To update megan @@ -14850,6 +15820,7 @@ Sequence analysis MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. + To update https://github.com/husonlab/megan-ce Sequence Analysis @@ -14870,6 +15841,7 @@ Sequence analysis, Genetic variation, Statistics and probability, Data mining The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. + To update http://meme-suite.org/ ChIP-seq @@ -14890,6 +15862,7 @@ Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. + To update http://meme-suite.org/ ChIP-seq @@ -14910,6 +15883,7 @@ Assign sequence type to N. meningitidis genome assemblies + Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis @@ -14930,6 +15904,7 @@ GWAS study, Mapping Pedigree Analysis package Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation + Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis @@ -14950,6 +15925,7 @@ Sequence assembly, Whole genome sequencing, Plant biology Merqury is a tool for evaluating genomes assemblies based of k-mer operations. Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. + Up-to-date https://github.com/marbl/merqury Assembly @@ -14970,6 +15946,7 @@ Whole genome sequencing, Genomics, Sequence analysis, Sequencing Meryl a k-mer counter. Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. + Up-to-date https://github.com/marbl/meryl Assembly @@ -14990,6 +15967,7 @@ Metagenomics, Sequence assembly, Metagenomic sequencing MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning + Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics @@ -15010,6 +15988,7 @@ Metagenomics, Gene and protein families MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics + To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation @@ -15030,6 +16009,7 @@ Metagenomics, Sequencing metagenomeSeq Normalization Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. + To update Metagenomics @@ -15041,16 +16021,17 @@ metaphlan 4.0.6 - 4.0.6 + 4.1.0 metaphlan - Up-to-date + To update metaphlan MetaPhlAn Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics MetaPhlAn for Metagenomic Phylogenetic Analysis Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. - Up-to-date + + To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan @@ -15070,6 +16051,7 @@ Immunoproteins, genes and antigens, Sequence analysis mapper for full-length T- and B-cell repertoire sequencing Mapper for full-length T- and B-cell repertoire sequencing. + Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis @@ -15090,6 +16072,7 @@ Sequence assembly Short-read assembler based on a de Bruijn graph Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. + Up-to-date https://gatb.inria.fr/software/minia/ Assembly @@ -15110,6 +16093,7 @@ Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) + To update https://github.com/lh3/miniasm Assembly @@ -15130,6 +16114,7 @@ Mapping A fast pairwise aligner for genomic and spliced nucleotide sequences Pairwise aligner for genomic and spliced nucleotide sequences + Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers @@ -15150,6 +16135,7 @@ Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. + Up-to-date https://github.com/lh3/miniprot Sequence Analysis @@ -15170,6 +16156,7 @@ Computational detection of canonical microRNAs + Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis @@ -15190,6 +16177,7 @@ assemble mitochondrial genomes + Up-to-date https://github.com/chrishah/MITObim Assembly @@ -15210,6 +16198,7 @@ Zoology, Whole genome sequencing de-novo annotation of metazoan mitochondrial genomes De novo metazoan mitochondrial genome annotation. + To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis @@ -15230,6 +16219,7 @@ Immunoproteins, genes and antigens Scan contig files against PubMLST typing schemes Multi Locus Sequence Typing from an assembled genome or from a set of reads. + To update https://github.com/tseemann/mlst Sequence Analysis @@ -15250,6 +16240,7 @@ MOABS for differential methylation analysis on Bisulfite sequencing data. + To update https://github.com/sunnyisgalaxy/moabs Epigenetics @@ -15260,17 +16251,18 @@ mosdepth - 0.3.5 + 0.3.6 0.3.6 mosdepth - To update + Up-to-date fast and flexible BAM/CRAM depth calculation - To update + + Up-to-date https://github.com/brentp/mosdepth SAM mosdepth @@ -15290,6 +16282,7 @@ Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Mothur wrappers Open-source, platform-independent, community-supported software for describing and comparing microbial communities + To update https://www.mothur.org Metagenomics @@ -15310,6 +16303,7 @@ A multiple sequences alignment bootstrapping tool. + Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation @@ -15330,6 +16324,7 @@ Analyzes collections of multi-condition ChIP-seq data. + To update http://mahonylab.org/software/multigps/ ChIP-seq @@ -15340,17 +16335,18 @@ multigsea - 1.8.0 + 1.12.0 1.12.0 bioconductor-multigsea - To update + Up-to-date multiGSEA multiGSEA Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules GSEA-based pathway enrichment analysis for multi-omics data A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. - To update + + Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea @@ -15361,7 +16357,7 @@ multiqc 1.11 - 1.19 + 1.21 multiqc To update multiqc @@ -15370,6 +16366,7 @@ Sequencing, Bioinformatics MultiQC aggregates results from bioinformatics analyses across many samples into a single report MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization @@ -15390,6 +16387,7 @@ Sequence analysis, Human genetics Mummer4 Tools System for rapidly aligning large DNA sequences to one another. + Up-to-date https://github.com/mummer4/mummer Sequence Analysis @@ -15410,6 +16408,7 @@ Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Antibiotic resistance predictions Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed + To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis @@ -15430,6 +16429,7 @@ Proteomics, Metabolomics, Proteomics experiment, Small molecules mass-spectrometry data processing, with the main focus on LC-MS data Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. + Up-to-date http://mzmine.github.io/ Metabolomics @@ -15450,6 +16450,7 @@ nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) + Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis @@ -15470,6 +16471,7 @@ Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro + To update https://nanocompore.rna.rocks/ Sequence Analysis @@ -15490,6 +16492,7 @@ Plotting tool for long read sequencing data and alignments + To update https://github.com/wdecoster/NanoPlot Visualization @@ -15510,6 +16513,7 @@ NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. + To update https://a-slide.github.io/NanopolishComp Sequence Analysis @@ -15530,6 +16534,7 @@ Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API + Up-to-date https://github.com/kblin/ncbi-acc-download Data Source @@ -15550,6 +16555,7 @@ Biological databases NCBI datasets downloads biological sequence data across all domains of life from NCBI. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. + To update https://github.com/ncbi/datasets Data Source @@ -15570,6 +16576,7 @@ NCBI Entrez Direct allow fetching data from NCBI Databases + Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source @@ -15590,6 +16597,7 @@ NCBI Entrez E-Utilties allow fetching data from NCBI Databases + To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source @@ -15610,6 +16618,7 @@ FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). + Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis @@ -15630,6 +16639,7 @@ Sequence assembly Error correction and de-novo assembly for ONT Nanopore reads NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. + Up-to-date https://github.com/xiaochuanle/NECAT Assembly @@ -15650,6 +16660,7 @@ Phylogeny, Genomics, Computer science Perform operations on Newick trees The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. + To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics @@ -15670,6 +16681,7 @@ Identify differences between your sequences and a reference sequence used by Nextstrain + To update https://github.com/nextstrain/nextclade Sequence Analysis @@ -15690,6 +16702,7 @@ Sequencing, Mapping, DNA structural variation CoNvex Gap-cost alignMents for Long Reads An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. + Up-to-date https://github.com/philres/ngmlr Next Gen Mappers @@ -15710,6 +16723,7 @@ Genomics, Transcriptomics NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. NGSUtils is a suite of software tools for working with next-generation sequencing datasets + To update https://github.com/ngsutils/ngsutils SAM @@ -15730,6 +16744,7 @@ Estimate average coverage in metagenomic datasets + To update http://nonpareil.readthedocs.io Metagenomics @@ -15741,7 +16756,7 @@ novoplasty 4.3.1 - 4.3.3 + 4.3.5 novoplasty To update @@ -15750,6 +16765,7 @@ NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. + To update https://github.com/ndierckx/NOVOPlasty Assembly @@ -15770,6 +16786,7 @@ Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. + Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics @@ -15790,6 +16807,7 @@ Sequence analysis, DNA, Sequencing OBITools is a set of programs developed to simplify the manipulation of sequence files Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. + Up-to-date http://metabarcoding.org/obitools Sequence Analysis @@ -15810,6 +16828,7 @@ Variant detection of SNVs + Up-to-date https://github.com/karel-brinda/ococo Variant Analysis @@ -15828,20 +16847,42 @@ - Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. + Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. + + + To update + https://github.com/vgteam/odgi + Sequence Analysis + + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ + + + + omark + 0.3.0 + + + To update + + + + + Proteome quality assessment software + To update - https://github.com/vgteam/odgi + https://github.com/DessimozLab/OMArk Sequence Analysis - + omark iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ + https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ ont_fast5_api 3.1.3 - 4.1.2 + 4.1.3 ont-fast5-api To update @@ -15850,6 +16891,7 @@ ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. + To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore @@ -15870,6 +16912,7 @@ ONTO-Toolkit is a collection of tools for managing ontologies. + Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation @@ -15890,6 +16933,7 @@ Optimal Design Of Experiment + To update https://github.com/pablocarb/doebase Synthetic Biology @@ -15910,6 +16954,7 @@ Precision HLA typing from NGS data + Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis @@ -15930,6 +16975,7 @@ Computer science, RNA-Seq, Transcriptomics, Small molecules Galaxy wrapper for ORFIPY A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. + Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis @@ -15950,6 +16996,7 @@ Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Accurate inference of orthologous gene groups made easy OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. + Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis @@ -15970,6 +17017,7 @@ Tool to make cached genome annotation data available as a list of datasets collection + To update Data Source @@ -15990,6 +17038,7 @@ Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. + Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis @@ -16010,6 +17059,7 @@ Filtering blast out from querying assembly against mitochondrial database. + Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis @@ -16030,6 +17080,7 @@ Molecular interactions, pathways and networks, Systems biology, Data visualisation Pathview is a tool set for pathway based data integration and visualization. Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. + To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis @@ -16050,6 +17101,7 @@ Mapping Compute genomic consensus and call variants using PacBio reads mapped to a reference The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. + Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis @@ -16060,17 +17112,18 @@ pbmm2 - 1.10.0 + 1.13.1 1.13.1 pbmm2 - To update + Up-to-date pbmm2 pbmm2 Pairwise sequence alignment, Sorting Mapping A minimap2 SMRT wrapper for PacBio data. pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. - To update + + Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 @@ -16090,6 +17143,7 @@ Contains a tool that produces an insert size histogram for a paired-end BAM file. + To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics @@ -16097,6 +17151,27 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram + + + peakzilla + 1.0 + + python + To update + + + + + Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. + + + To update + https://github.com/steinmann/peakzilla + ChIP-seq + peakzilla + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla + pear @@ -16110,6 +17185,7 @@ Sequence assembly PEAR evaluates all possible paired-end read overlaps Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. + Up-to-date @@ -16130,6 +17206,7 @@ rapid standardised annotation tool for bacteriophage genomes and metagenomes + To update https://github.com/gbouras13/pharokka Genome annotation @@ -16144,11 +17221,12 @@ 1.46.0 bioconductor-phyloseq To update - - - - + phyloseq + phyloseq + Deposition, Analysis, Visualisation + Microbiology, Sequence analysis, Metagenomics Handling and analysis of high-throughput microbiome census data + Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html @@ -16170,6 +17248,7 @@ Phylogenetics, Bioinformatics, Phylogenetics PhyML is a phylogeny software based on the maximum-likelihood principle. Phylogenetic estimation software using Maximum Likelihood + Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics @@ -16180,17 +17259,18 @@ picard - 2.18.2 + 3.1.1 3.1.1 picard - To update + Up-to-date picard_fastqtosam picard_fastqtosam Formatting Sequencing Picard SAM/BAM manipulation tools. Create an unaligned BAM file. - To update + + Up-to-date http://broadinstitute.github.io/picard/ SAM picard @@ -16210,6 +17290,7 @@ Compose a text parameter value using text, integer and float values + To update Text Manipulation @@ -16224,11 +17305,12 @@ 1.1.4 picrust To update - - - - + picrust + PICRUSt + Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding + Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing PICRUSt wrappers + PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. To update https://picrust.github.io/picrust/ @@ -16250,6 +17332,7 @@ Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + To update https://github.com/picrust/picrust2/wiki Metagenomics @@ -16270,6 +17353,7 @@ Assembly pilon is a tool for assembly improvement and variant analysis in bacteria Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. + To update Variant Analysis @@ -16290,6 +17374,7 @@ Multipe sequence alignment + Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers @@ -16310,6 +17395,7 @@ Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. + To update https://github.com/pmelsted/pizzly/ Transcriptomics @@ -16330,6 +17416,7 @@ PlasFlow - Prediction of plasmid sequences in metagenomic contigs. + Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis @@ -16350,6 +17437,7 @@ Whole genome sequencing, Sequence assembly, Mapping, Probes and primers "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). + Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis @@ -16370,6 +17458,7 @@ GWAS study PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study @@ -16390,6 +17479,7 @@ Sequence assembly, Sequence composition, complexity and repeats, Mapping "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. + To update https://github.com/rrwick/Polypolish Sequence Analysis @@ -16410,6 +17500,7 @@ Porechop - Finding and removing adapters from Oxford Nanopore reads + To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation @@ -16430,6 +17521,7 @@ DNA, Sequencing A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. + Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation @@ -16450,6 +17542,7 @@ Sequencing, DNA, Immunology pRESTO toolkit for immune repertoire analysis. Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. + To update https://presto.readthedocs.io/ Sequence Analysis @@ -16460,9 +17553,9 @@ pretext - 0.1.9 - 0.1.9 - pretextmap + 0.0.6 + 0.0.6 + pretextgraph Up-to-date @@ -16470,6 +17563,7 @@ Process genome contacts maps processing images. + Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis @@ -16490,6 +17584,7 @@ Transcriptomics, Metagenomics, Genomics PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. + To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics @@ -16510,6 +17605,7 @@ Mauve/ProgressiveMauve Multiple Sequence Aligner + To update Sequence Analysis @@ -16530,6 +17626,7 @@ Genomics, Model organisms, Virology Rapid annotation of prokaryotic genomes Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. + Up-to-date http://github.com/tseemann/prokka Sequence Analysis @@ -16550,6 +17647,7 @@ Protein annotation of short human readable descriptions + To update https://github.com/usadellab/prot-scriber Proteomics @@ -16570,6 +17668,7 @@ Phylogeny Proteinortho is a tool to detect orthologous proteins/genes within different species. Proteinortho is a tool to detect orthologous genes within different species + Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics @@ -16590,6 +17689,7 @@ PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. + Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics @@ -16610,6 +17710,7 @@ PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data + To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq @@ -16630,6 +17731,7 @@ Sequence assembly Purge haplotigs and overlaps in an assembly based on read depth Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences + Up-to-date https://github.com/dfguan/purge_dups Assembly @@ -16650,6 +17752,7 @@ QC metrics for ONT Basecalling + Up-to-date https://github.com/tleonardi/pycoQC Nanopore @@ -16670,6 +17773,7 @@ EGA python client uses the EGA REST API to download authorized datasets and files. + To update https://github.com/EGA-archive/ega-download-client Data Source @@ -16690,6 +17794,7 @@ pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. + Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization @@ -16710,6 +17815,7 @@ Sequencing, Gene transcripts, Bioinformatics pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. + To update https://github.com/saketkc/pysradb Sequence Analysis @@ -16730,6 +17836,7 @@ Filter sequencing data + To update https://github.com/veg/qfilt Fastq Manipulation @@ -16750,6 +17857,7 @@ QIIME to perform microbial community analysis + To update http://www.qiime.org Metagenomics @@ -16770,6 +17878,7 @@ QIIME to perform microbial community analysis + To update http://www.qiime.org Metagenomics @@ -16790,6 +17899,7 @@ + To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis @@ -16810,6 +17920,7 @@ Data quality management Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. + To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM @@ -16830,6 +17941,7 @@ Sequence assembly Quast (Quality ASsessment Tool) evaluates genome assemblies. QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. + Up-to-date http://quast.bioinf.spbau.ru/ Assembly @@ -16850,6 +17962,7 @@ Contains a tool to query the IMPC database. + To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services @@ -16870,6 +17983,7 @@ Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output + To update Text Manipulation @@ -16890,6 +18004,7 @@ Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Merge long-read and hybrid assemblies to increase contiguity Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. + Up-to-date https://github.com/mahulchak/quickmerge Assembly @@ -16910,6 +18025,7 @@ RaceID3, StemID2, FateID - scRNA analysis + To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics @@ -16930,6 +18046,7 @@ Sequence assembly Reference-guided scaffolding of draft genomes tool. RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. + Up-to-date https://github.com/malonge/RagTag Assembly @@ -16950,6 +18067,7 @@ Phylogeny Galaxy wrapper for the RapidNJ tool A tool for fast canonical neighbor-joining tree construction. + Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics @@ -16957,6 +18075,27 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj + + + rasusa + 0.8.0 + 0.8.0 + rasusa + Up-to-date + rasusa + rasusa + + + Randomly subsample sequencing reads to a specified coverage + Produces an unbiased subsample of your reads + + Up-to-date + https://github.com/mbhall88/rasusa + Sequence Analysis + rasusa + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa + raven @@ -16970,6 +18109,7 @@ Raven is a de novo genome assembler for long uncorrected reads. + To update https://github.com/lbcb-sci/raven Assembly @@ -16990,6 +18130,7 @@ Phylogenetics, Sequence analysis RAxML - A Maximum Likelihood based phylogenetic inference A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics @@ -17010,6 +18151,7 @@ RNA, RNA-Seq, Sequencing Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. + To update https://github.com/mourisl/Rcorrector Fastq Manipulation @@ -17030,6 +18172,7 @@ Rapid decontamination of SARS-CoV-2 sequencing reads + To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis @@ -17040,8 +18183,8 @@ recentrifuge - 1.13.2 - 1.13.2 + 1.14.0 + 1.14.0 recentrifuge Up-to-date Recentrifuge @@ -17050,6 +18193,7 @@ Metagenomics, Microbial ecology, Metagenomic sequencing "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." Robust comparative analysis and contamination removal for metagenomics. + Up-to-date https://github.com/khyox/recentrifuge Metagenomics @@ -17070,6 +18214,7 @@ Red (REpeat Detector) + Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis @@ -17090,6 +18235,7 @@ Sequence analysis, Sequence composition, complexity and repeats RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). + Up-to-date http://www.repeatmasker.org/ Sequence Analysis @@ -17110,6 +18256,7 @@ RepeatModeler - Model repetitive DNA + To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation @@ -17130,6 +18277,7 @@ Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. + To update ChIP-seq @@ -17150,6 +18298,7 @@ Flexibly restructure and aggregate data using just the two functions melt and dcast + To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation @@ -17170,6 +18319,7 @@ Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. + To update Genomic Interval Operations @@ -17190,6 +18340,7 @@ multi-block analysis + To update https://github.com/rgcca-factory/RGCCA Statistics @@ -17200,8 +18351,8 @@ rgrnastar - 2.7.10b 2.7.11a + 2.7.11b star To update star @@ -17210,6 +18361,7 @@ RNA-Seq, Transcriptomics RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper Ultrafast universal RNA-seq data aligner + To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics @@ -17230,6 +18382,7 @@ Computational biology Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. + To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA @@ -17250,6 +18403,7 @@ Sequence assembly, Transcriptomics, RNA-seq rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. Quality assessment tool for de novo transcriptome assemblies. + Up-to-date https://github.com/ablab/rnaquast Assembly, RNA @@ -17270,6 +18424,7 @@ DNA, Genomics, Mapping Roary the pangenome pipeline A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. + Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis @@ -17290,6 +18445,7 @@ Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output + To update https://github.com/brsynth/rp2biosensor Synthetic Biology @@ -17310,6 +18466,7 @@ Enumerate and seperate the different pathways generated by RetroPath2.0 + To update https://github.com/brsynth/rp2paths Synthetic Biology @@ -17320,7 +18477,7 @@ rpbasicdesign - 1.1.1 + 1.2.2 rpbasicdesign To update @@ -17330,6 +18487,7 @@ Extracting enzyme IDs from rpSBML files + To update https://github.com/brsynth/rpbasicdesign Synthetic Biology @@ -17350,6 +18508,7 @@ Perform FBA for the RetroPath2.0 heterologous pathways + To update https://github.com/brsynth/rptools/releases Synthetic Biology @@ -17370,6 +18529,7 @@ Suite of tools that work on rpSBML format + To update https://github.com/brsynth/rptools Synthetic Biology @@ -17390,6 +18550,7 @@ Reaction Rules Parser + To update https://github.com/brsynth/RRParser Synthetic Biology @@ -17410,6 +18571,7 @@ Sequencing an RNA-seq quality control package Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. + To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization @@ -17430,6 +18592,7 @@ Gene expression, RNA-seq Remove Unwanted Variation from RNA-Seq Data This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. + To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics @@ -17450,6 +18613,7 @@ Sequence assembly, DNA binding sites, Mapping A tool to scaffold long read assemblies with Hi-C > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch + Up-to-date https://github.com/marbl/SALSA Assembly @@ -17470,6 +18634,7 @@ DNA, Sequencing, Mapping samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files A tool to mark duplicates and extract discordant and split reads from SAM files. + To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis @@ -17481,16 +18646,17 @@ sansa 0.0.8 - 0.0.8 + 0.1.1 sansa - Up-to-date + To update Sansa is a tool for structural variant annotation. - Up-to-date + + To update https://github.com/dellytools/sansa Variant Analysis sansa @@ -17510,6 +18676,7 @@ sarscov2formatter custom script + Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis @@ -17530,6 +18697,7 @@ sarscov2summary custom script + To update https://github.com/nickeener/sarscov2summary Sequence Analysis @@ -17550,6 +18718,7 @@ Convert SBML to SBOL format + To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology @@ -17570,6 +18739,7 @@ Gene expression, Cell biology, Genetics Scanpy – Single-Cell Analysis in Python Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. + To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis @@ -17590,6 +18760,7 @@ RNA-seq, Quality affairs, Molecular genetics Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. + To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization @@ -17610,6 +18781,7 @@ Converter between difference single-cell formats + Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics @@ -17630,6 +18802,7 @@ scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. + To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization @@ -17650,6 +18823,7 @@ scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics + Up-to-date http://scikit-bio.org/ Sequence Analysis @@ -17670,6 +18844,7 @@ Scoary calculates the assocations between all genes in the accessory genome and the traits. + Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics @@ -17690,6 +18865,7 @@ Gene expression, RNA-seq, Sequencing A flexible preprocessing pipeline for single-cell RNA-sequencing data A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. + To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics @@ -17710,6 +18886,7 @@ SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. + Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq @@ -17730,6 +18907,7 @@ Performs enzyme selection from a reaction query. + Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology @@ -17750,6 +18928,7 @@ Metagenomics, Machine learning, Microbial ecology, Sequence assembly SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. + Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics @@ -17770,6 +18949,7 @@ Transcriptomics, Mapping Precision HLA typing and expression from RNAseq data seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. + Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis @@ -17790,6 +18970,7 @@ Sequence complexity for raw reads + Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis @@ -17801,7 +18982,7 @@ seqkit 2.3.1 - 2.6.1 + 2.7.0 seqkit To update seqkit @@ -17810,6 +18991,7 @@ Database management, Sequence analysis A cross-platform and ultrafast toolkit for FASTA/Q file manipulation FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. + To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis @@ -17817,6 +18999,27 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit + + + seqprep + 1.3.2 + 1.3.2 + seqprep + Up-to-date + seqprep + SeqPrep + Nucleic acid design + Genomics, Sequence assembly, Sequencing, Probes and primers + Tool for merging paired-end Illumina reads and trimming adapters. + Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. + + Up-to-date + https://github.com/jstjohn/SeqPrep + Fastq Manipulation, Sequence Analysis + seqprep + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep + seqsero2 @@ -17830,6 +19033,7 @@ Salmonella serotype prediction from genome sequencing data + Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis @@ -17850,6 +19054,7 @@ Data management Toolkit for processing sequences in FASTA/Q formats A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. + Up-to-date https://github.com/lh3/seqtk Sequence Analysis @@ -17870,6 +19075,7 @@ Alignment to variation graph inducer + To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis @@ -17890,6 +19096,7 @@ A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data + To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics @@ -17910,6 +19117,7 @@ Fast de novo assembly of long read sequencing data + To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore @@ -17930,6 +19138,7 @@ Metagenomics, Sequencing, Genetics Reconstruct haplotypes using ShoRAH in amplicon mode Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. + To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis @@ -17950,6 +19159,7 @@ Genomics, Microbiology, Sequence assembly Faster de novo assembly pipeline based around Spades Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. + Up-to-date https://github.com/tseemann/shovill Assembly @@ -17970,6 +19180,7 @@ Data quality management A windowed adaptive trimming tool for FASTQ files using quality A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. + To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis @@ -17990,6 +19201,7 @@ A text mining framework for interactive analysis and visualization of similarities among biomedical entities. + To update https://github.com/dlal-group/simtext Text Manipulation @@ -18010,6 +19222,7 @@ Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy SINA reference based multiple sequence alignment Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment + Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis @@ -18030,6 +19243,7 @@ Sinto single-cell analysis tools + To update https://github.com/timoast/sinto Sequence Analysis @@ -18050,6 +19264,7 @@ Slamdunk maps and quantifies SLAMseq reads + Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers @@ -18070,6 +19285,7 @@ RNA-seq, Gene expression, Statistics and probability Sleuth is a program for differential analysis of RNA-Seq data. A statistical model and software application for RNA-seq differential expression analysis. + Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics @@ -18090,6 +19306,7 @@ Genomics, Population genetics, Workflows, Virology, Sequencing Set of utilities for manipulating small viral genome data. Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. + Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis @@ -18110,6 +19327,7 @@ Sequence assembly, Genetic variation, Mathematics Inference of ploidy and heterozygosity structure using whole genome sequencing Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 + Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly @@ -18130,6 +19348,7 @@ DNA, DNA polymorphism, Genetics SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. + Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis @@ -18150,6 +19369,7 @@ DNA structural variation, Sequencing Galaxy wrapper for sniffles An algorithm for structural variation detection from third generation sequencing alignment. + To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis @@ -18170,6 +19390,7 @@ Virology Summarise snps relative to a reference sequence Summarise snps relative to a reference sequence + Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis @@ -18190,6 +19411,7 @@ Genomics, Model organisms, DNA polymorphism, Phylogenetics Contains the snippy tool for characterising microbial snps Rapid haploid variant calling and core SNP phylogeny generation. + To update https://github.com/tseemann/snippy Sequence Analysis @@ -18210,6 +19432,7 @@ Compute pairwise SNP distance matrix from a FASTA sequence alignment + Up-to-date https://github.com/tseemann/snp-dists Variant Analysis @@ -18230,6 +19453,7 @@ Finds SNP sites from a multi-FASTA alignment file + Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis @@ -18250,6 +19474,7 @@ DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). + To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis @@ -18270,6 +19495,7 @@ Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis @@ -18290,6 +19516,7 @@ Order and orientation of complete bacterial genomes + To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis @@ -18310,6 +19537,7 @@ Scripts for parsing Mykrobe predict results for Shigella sonnei. + Up-to-date https://github.com/katholt/sonneityping Sequence Analysis @@ -18324,11 +19552,12 @@ 3.15.5 spades Up-to-date - - - - + biosyntheticspades + biosyntheticSPAdes + Sequence assembly + Sequence assembly, Sequence sites, features and motifs, Genetic engineering SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. + biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads Up-to-date https://github.com/ablab/spades @@ -18350,6 +19579,7 @@ Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. + To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation @@ -18370,6 +19600,7 @@ Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. + Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis @@ -18390,6 +19621,7 @@ Wavelet analysis for 3d-image stacks + To update http://github.com/tensionhead/spyboat Imaging, Graphics @@ -18410,6 +19642,7 @@ DNA, Genomics, Sequencing NCBI Sequence Read Archive toolkit utilities The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. + To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation @@ -18430,6 +19663,7 @@ SRST2 Short Read Sequence Typing for Bacterial Pathogens + To update http://katholt.github.io/srst2/ Metagenomics @@ -18450,6 +19684,7 @@ Mapping, Population genetics Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. + To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis @@ -18470,6 +19705,7 @@ Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq + To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis @@ -18490,6 +19726,7 @@ STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR + To update Sequence Analysis, Transcriptomics @@ -18510,6 +19747,7 @@ Toolbox to optimize biological model + Up-to-date https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology @@ -18530,6 +19768,7 @@ + Up-to-date https://github.com/Illumina/strelka/ Variant Analysis @@ -18550,6 +19789,7 @@ Transcriptomics, RNA-seq StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. + Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics @@ -18570,6 +19810,7 @@ Population genetics for using multi-locus genotype data to investigate population structure. The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. + Up-to-date Phylogenetics, Variant Analysis @@ -18590,6 +19831,7 @@ for parsing STRUCTURE outputs and for performing the Evanno method + Up-to-date Phylogenetics, Variant Analysis @@ -18610,6 +19852,7 @@ Parallel MCMC Linkage Analysis + Up-to-date https://github.com/ajm/swiftlink Variant Analysis @@ -18621,7 +19864,7 @@ syndiva 1.0 - 1.2.4 + clustalo To update @@ -18630,6 +19873,7 @@ SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. + To update Proteomics @@ -18650,6 +19894,7 @@ Perform general-purpose table operations + To update Text Manipulation @@ -18670,6 +19915,7 @@ Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. + To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations @@ -18690,6 +19936,7 @@ Analysis of positional mismatches + Up-to-date Sequence Analysis @@ -18710,6 +19957,7 @@ Filter RefSeq by taxonomy + To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation @@ -18730,6 +19978,7 @@ Metagenomics Krona pie chart from taxonomic profile Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). + To update http://sourceforge.net/projects/krona/ Assembly @@ -18750,6 +19999,7 @@ Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. + To update https://github.com/jodyphelan/TBProfiler Sequence Analysis @@ -18770,6 +20020,7 @@ M. tuberculosis H37Rv VCF filter + Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis @@ -18790,6 +20041,7 @@ Table to GFF3 + To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis @@ -18810,6 +20062,7 @@ Generate HTML report from SnpEff M.tuberculosis VCF(s) + Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis @@ -18830,6 +20083,7 @@ Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Transposable element insertions finder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. + To update https://github.com/VistaSohrab/TEfinder Sequence Analysis @@ -18850,6 +20104,7 @@ RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Single locus resolution of Transposable ELEment expression. Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. + Up-to-date https://github.com/mlbendall/telescope/ Genome annotation @@ -18870,6 +20125,7 @@ The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. + Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis @@ -18890,6 +20146,7 @@ Type a specific transposable element (TE) of interest from paired-end sequencing data. + Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis @@ -18910,6 +20167,7 @@ Compute distances between sequences + To update https://github.com/veg/tn93/ Sequence Analysis @@ -18930,6 +20188,7 @@ + To update @@ -18950,6 +20209,7 @@ Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing TransDecoder finds coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + To update https://transdecoder.github.io/ Transcriptomics, RNA @@ -18970,6 +20230,7 @@ DNA, Sequencing, Mobile genetic elements TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. + To update https://github.com/mad-lab/transit/ Genome annotation @@ -18990,6 +20251,7 @@ Finds rho-independent transcription terminators in bacterial genomes + To update Sequence Analysis @@ -19010,6 +20272,7 @@ A flexible read trimming tool for Illumina NGS data + Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation @@ -19030,6 +20293,7 @@ Transcriptomics, Gene expression, Gene transcripts Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. + Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA @@ -19050,6 +20314,7 @@ Gene expression, Transcriptomics Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. + To update https://trinotate.github.io/ Transcriptomics, RNA @@ -19070,6 +20335,7 @@ Trycycler toolkit wrappers + Up-to-date https://github.com/rrwick/Trycycler Assembly @@ -19080,17 +20346,18 @@ tsebra - 1.1.2 - 1.1.2.2 + 1.1.2.3 + 1.1.2.3 tsebra - To update + Up-to-date This tool has been developed to combine BRAKER predictions. - To update + + Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation @@ -19110,6 +20377,7 @@ T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation + To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation @@ -19130,6 +20398,7 @@ Transcriptomics, Gene transcripts, Workflows Wrapper for the Bioconductor package tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. + To update http://bioconductor.org/packages/tximport/ Transcriptomics @@ -19150,6 +20419,7 @@ Sequence analysis Standalone blat sequence search command line tool Fast, accurate spliced alignment of DNA sequences. + To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis @@ -19170,6 +20440,7 @@ Sequence analysis faSplit is a tool to split a single FASTA file into several files Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation @@ -19190,6 +20461,7 @@ Sequence analysis Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats @@ -19210,6 +20482,7 @@ Sequence analysis twoBitToFa is a tool to convert all or part of .2bit file to FASTA Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats @@ -19230,6 +20503,7 @@ Sequence analysis converts bedGraph (wig) files into binary bigwig Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats @@ -19241,7 +20515,7 @@ umi_tools 1.1.2 - 1.1.4 + 1.1.5 umi_tools To update umi-tools @@ -19250,6 +20524,7 @@ NGS, Sequence sites, features and motifs, Quality affairs UMI-tools extract - Extract UMIs from fastq Tools for handling Unique Molecular Identifiers in NGS data sets. + To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics @@ -19270,6 +20545,7 @@ Microbiology, Genomics, Sequencing, Sequence assembly Unicycler is a hybrid assembly pipeline for bacterial genomes. A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. + Up-to-date https://github.com/rrwick/Unicycler Assembly @@ -19290,6 +20566,7 @@ UShER toolkit wrappers + To update https://github.com/yatisht/usher Phylogenetics @@ -19310,6 +20587,7 @@ A pipeline for detecting mis-assemblies in metagenomic assemblies. + To update https://github.com/marbl/VALET Metagenomics @@ -19330,6 +20608,7 @@ Whole genome sequencing, Mapping, Sequence assembly Classify Influenza samples from raw short read sequence data VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. + Up-to-date https://github.com/connor-lab/vapor Sequence Analysis @@ -19350,6 +20629,7 @@ VarDict - calls SNVs and indels for tumour-normal pairs + To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis @@ -19370,6 +20650,7 @@ Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data + To update Variant Analysis @@ -19390,6 +20671,7 @@ VarScan is a variant caller for high-throughput sequencing data + To update https://dkoboldt.github.io/varscan/ Variant Analysis @@ -19410,6 +20692,7 @@ Virology Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. + Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis @@ -19430,6 +20713,7 @@ vcf2maf: Convert VCF into MAF + Up-to-date Convert Formats @@ -19440,17 +20724,18 @@ vcfanno - 0.3.3 + 0.3.5 0.3.5 vcfanno - To update + Up-to-date vcfanno vcfanno SNP annotation Genetic variation, Data submission, annotation and curation Annotate VCF files Fast, flexible annotation of genetic variants. - To update + + Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno @@ -19470,6 +20755,7 @@ + To update https://cran.r-project.org/package=vegan Metagenomics @@ -19490,6 +20776,7 @@ Velocyto is a library for the analysis of RNA velocity. + Up-to-date http://velocyto.org/ Transcriptomics @@ -19510,6 +20797,7 @@ Sequence assembly de novo genomic assembler specially designed for short read sequencing technologies A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. + To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly @@ -19530,6 +20818,7 @@ Genomics, Sequence assembly Automatically optimize Velvet assemblies This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. + To update Assembly @@ -19541,7 +20830,7 @@ verkko 1.3.1 - 1.4.1 + 2.0 verkko To update @@ -19550,6 +20839,7 @@ Telomere-to-telomere assembly pipeline + To update https://github.com/marbl/verkko Assembly @@ -19561,7 +20851,7 @@ vg 1.23.0 - 1.54.0 + 1.55.0 vg To update @@ -19570,6 +20860,7 @@ Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods + To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis @@ -19590,6 +20881,7 @@ Virology Deep Learning method for novel virus detection in sequencing data VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). + To update https://github.com/cbib/virhunter Machine Learning @@ -19610,6 +20902,7 @@ Tool to create a Volcano Plot + To update Visualization, Transcriptomics, Statistics @@ -19630,6 +20923,7 @@ Metagenomics, Sequence analysis VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + To update https://github.com/torognes/vsearch Sequence Analysis @@ -19650,6 +20944,7 @@ The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. + To update https://github.com/USDA-VS/vSNP Sequence Analysis @@ -19670,6 +20965,7 @@ provides simple weather in text format + To update http://wttr.in/ Visualization, Web Services @@ -19690,6 +20986,7 @@ Nucleic acid sites, features and motifs, Sequence analysis Sequence Logo generator for fasta Web-based application designed to make generate sequence logos. + To update Graphics @@ -19710,6 +21007,7 @@ Identify repetitive regions using WindowMasker + To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis @@ -19730,6 +21028,7 @@ A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. + Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers @@ -19750,6 +21049,7 @@ XPath XML querying tool + To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation @@ -19770,6 +21070,7 @@ Yet Another Hi-C scaffolding tool + Up-to-date https://github.com/c-zhou/yahs Assembly @@ -19790,6 +21091,7 @@ ChIP-seq discretization and quality control + Up-to-date https://github.com/nanakiksc/zerone ChIP-seq @@ -19810,6 +21112,7 @@ Operate on and transform BAM datasets in various ways using bamtools + Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM @@ -19830,6 +21133,7 @@ Filter BAM datasets on various attributes using bamtools filter + Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM @@ -19850,6 +21154,7 @@ + Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM @@ -19870,6 +21175,7 @@ Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. + Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation @@ -19890,6 +21196,7 @@ Galaxy wrappers for the Cuffcompare tool. + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -19910,6 +21217,7 @@ Galaxy wrappers for the Cuffdiff tool. + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -19930,6 +21238,7 @@ Galaxy wrappers for the Cufflinks tool. + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -19950,6 +21259,7 @@ Galaxy wrappers for the Cuffmerge tool. + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -19970,6 +21280,7 @@ The Cuffnorm tool + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -19990,6 +21301,7 @@ The Cuffquant tool + Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics @@ -20010,6 +21322,7 @@ Length Distribution chart + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics @@ -20030,6 +21343,7 @@ FASTA Width formatter + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation @@ -20050,6 +21364,7 @@ RNA/DNA converter. + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation @@ -20070,6 +21385,7 @@ Draw quality score boxplot + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics @@ -20090,6 +21406,7 @@ Quality format converter (ASCII-Numeric) + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation @@ -20110,6 +21427,7 @@ Filter by quality + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation @@ -20130,6 +21448,7 @@ FASTQ to FASTA converter + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats @@ -20150,6 +21469,7 @@ Remove sequencing artifacts + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation @@ -20170,6 +21490,7 @@ Barcode Splitter + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation @@ -20190,6 +21511,7 @@ Clip adapter sequences + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation @@ -20210,6 +21532,7 @@ Collapse sequences + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation @@ -20230,6 +21553,7 @@ Draw nucleotides distribution chart + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics @@ -20250,6 +21574,7 @@ Compute quality statistics + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics @@ -20270,6 +21595,7 @@ Rename sequences + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation @@ -20290,6 +21616,7 @@ Reverse-Complement + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation @@ -20310,6 +21637,7 @@ Trim sequences + Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation @@ -20330,6 +21658,7 @@ Combine FASTA and QUAL into FASTQ + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation @@ -20350,6 +21679,7 @@ Filter FASTQ reads by quality score and length + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20370,6 +21700,7 @@ Convert between various FASTQ quality formats. + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20390,6 +21721,7 @@ Manipulate FASTQ reads on various attributes. + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20410,6 +21742,7 @@ FASTQ Masker by quality score + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20430,6 +21763,7 @@ FASTQ de-interlacer on paired end reads. + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20450,6 +21784,7 @@ FASTQ interlacer on paired end reads + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20470,6 +21805,7 @@ FASTQ joiner on paired end reads + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20490,6 +21826,7 @@ FASTQ splitter on joined paired end reads + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20510,6 +21847,7 @@ FASTQ Summary Statistics by column + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20530,6 +21868,7 @@ FASTQ to Tabular converter + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20550,6 +21889,7 @@ FASTQ Trimmer by quality + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20570,6 +21910,7 @@ FASTQ to FASTA converter + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20590,6 +21931,7 @@ Tabular to FASTQ converter + Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation @@ -20610,6 +21952,7 @@ Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. + To update http://ccb.jhu.edu/software/kraken/ Metagenomics @@ -20624,11 +21967,12 @@ 2.1.3 kraken2 To update - - - - + kraken2 + kraken2 + Taxonomic classification + Taxonomy, Metagenomics Kraken2 for taxonomic designation. + Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. To update http://ccb.jhu.edu/software/kraken/ @@ -20650,6 +21994,7 @@ + To update https://github.com/samtools/samtools SAM @@ -20670,6 +22015,7 @@ SnpEff is a genetic variant annotation and effect prediction toolbox + To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis @@ -20690,6 +22036,7 @@ snpEff SnpSift tools from Pablo Cingolani + To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis @@ -20710,6 +22057,7 @@ snpEff SnpSift dbnsfp tool from Pablo Cingolani + To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis @@ -20730,6 +22078,7 @@ Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome + To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis @@ -20750,6 +22099,7 @@ Converts VCF files into tab-delimited format + To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats @@ -20770,6 +22120,7 @@ Adds info fields from the second dataset which are not present in the first dataset. + To update https://github.com/ekg/vcflib Variant Analysis @@ -20790,6 +22141,7 @@ Splits alleleic primitives (gaps or mismatches) into multiple VCF lines + To update https://github.com/ekg/vcflib Variant Analysis @@ -20810,6 +22162,7 @@ Intersect VCF records with BED annotations + To update https://github.com/ekg/vcflib Variant Analysis @@ -20830,6 +22183,7 @@ Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. + To update https://github.com/ekg/vcflib Variant Analysis @@ -20850,6 +22204,7 @@ Intersect VCF and BED datasets + To update https://github.com/ekg/vcflib Variant Analysis @@ -20870,6 +22225,7 @@ Break multiple alleles into multiple records, or combine overallpoing alleles into a single record + To update https://github.com/ekg/vcflib Variant Analysis @@ -20890,6 +22246,7 @@ Verify that the reference allele matches the reference genome + To update https://github.com/ekg/vcflib Variant Analysis @@ -20910,6 +22267,7 @@ Combine multiple VCF datasets + To update https://github.com/ekg/vcflib Variant Analysis @@ -20930,6 +22288,7 @@ Output records belonging to samples commong between two datasets. + To update https://github.com/ekg/vcflib Variant Analysis @@ -20950,6 +22309,7 @@ Calculate distance to the nearest variant. + To update https://github.com/ekg/vcflib Variant Analysis @@ -20970,6 +22330,7 @@ Tool for filtering VCF files + To update https://github.com/ekg/vcflib Variant Analysis @@ -20990,6 +22351,7 @@ Count the allele frequencies across alleles present in each record in the VCF file. + To update https://github.com/ekg/vcflib Variant Analysis @@ -21010,6 +22372,7 @@ Removes multi-allelic sites by picking the most common alternate + To update https://github.com/ekg/vcflib Variant Analysis @@ -21030,6 +22393,7 @@ Convert genotype-based phased alleles into haplotype alleles + To update https://github.com/ekg/vcflib Variant Analysis @@ -21050,6 +22414,7 @@ Convert numerical representation of genotypes to allelic. + To update https://github.com/ekg/vcflib Variant Analysis @@ -21070,6 +22435,7 @@ Count the number of heterozygotes and alleles, compute het/hom ratio. + To update https://github.com/ekg/vcflib Variant Analysis @@ -21090,6 +22456,7 @@ Left-align indels and complex variants in VCF dataset + To update https://github.com/ekg/vcflib Variant Analysis @@ -21110,6 +22477,7 @@ Extract flanking sequences for each VCF record + To update https://github.com/ekg/vcflib Variant Analysis @@ -21130,6 +22498,7 @@ Randomly sample sites from VCF dataset + To update https://github.com/ekg/vcflib Variant Analysis @@ -21150,6 +22519,7 @@ Select samples from a VCF file + To update https://github.com/ekg/vcflib Variant Analysis @@ -21170,6 +22540,7 @@ Sort VCF dataset by coordinate + To update https://github.com/ekg/vcflib Variant Analysis @@ -21190,6 +22561,7 @@ Intersect two VCF datasets + To update https://github.com/ekg/vcflib Variant Analysis @@ -21210,6 +22582,7 @@ Thermo RAW file converter + To update https://github.com/compomics/ThermoRawFileParser Proteomics @@ -21230,6 +22603,7 @@ + To update @@ -21250,6 +22624,7 @@ Converts a BED file to a tabular list of exon locations + To update Proteomics @@ -21270,6 +22645,7 @@ NCBI BLAST+ with -remote option + To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis @@ -21290,6 +22666,7 @@ + To update http://proteowizard.sourceforge.net/ Proteomics @@ -21310,6 +22687,7 @@ Calgary approach to isotopes in proteomics + Up-to-date https://github.com/kinestetika/Calisp/ Proteomics @@ -21330,6 +22708,7 @@ Statistical and computational tools for analyzing mass spectrometry imaging datasets + To update http://cardinalmsi.org Proteomics, Metabolomics @@ -21350,6 +22729,7 @@ Protein Database Downloader + To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics @@ -21370,6 +22750,7 @@ Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. + To update Proteomics @@ -21390,6 +22771,7 @@ DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics + To update http://diaumpire.sourceforge.net/ Proteomics @@ -21410,6 +22792,7 @@ DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. + To update https://github.com/shubham1637/DIAlignR Proteomics @@ -21430,6 +22813,7 @@ DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. + To update https://github.com/vdemichev/DiaNN Proteomics @@ -21450,6 +22834,7 @@ diapysef is a convenience package for working with DIA-PASEF data + To update https://pypi.org/project/diapysef/ Proteomics @@ -21470,6 +22855,7 @@ Diffacto comparative protein abundance estimation + Up-to-date https://github.com/statisticalbiotechnology/diffacto Proteomics @@ -21490,6 +22876,7 @@ + To update @@ -21510,6 +22897,7 @@ + To update @@ -21530,6 +22918,7 @@ downloads eggnog data for eggnog-mapper + To update Proteomics @@ -21550,6 +22939,7 @@ download eggnog data for eggnog-mapper + To update Proteomics @@ -21570,6 +22960,7 @@ Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis eggnog-mapper fast functional annotation of novel sequences EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. + To update Proteomics @@ -21590,6 +22981,7 @@ Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis + To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics @@ -21610,6 +23002,7 @@ Concatenate FASTA database files together + To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation @@ -21630,6 +23023,7 @@ Generate FASTA from FASTG + To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics @@ -21650,6 +23044,7 @@ TRIC integrates information from all available runs via a graph-based alignment strategy + Up-to-date Proteomics @@ -21670,6 +23065,7 @@ Filter FASTA on the headers and/or the sequences + To update Fasta Manipulation, Proteomics @@ -21690,6 +23086,7 @@ FlashLFQ mass-spectrometry proteomics label-free quantification + To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics @@ -21710,6 +23107,7 @@ Filter and convert a gffCompare GTF to BED + To update https://github.com/gpertea/gffcompare/ Convert Formats @@ -21730,6 +23128,7 @@ Hardklör + To update Proteomics @@ -21750,6 +23149,7 @@ Convert mass spectrometry identification files on linux or MacOSX + To update Proteomics @@ -21770,6 +23170,7 @@ Enable protein summarisation and quantitation + To update https://github.com/compomics/LFQ_galaxy_p Proteomics @@ -21790,6 +23191,7 @@ + To update @@ -21810,6 +23212,7 @@ MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. + To update http://strimmerlab.org/software/maldiquant/ Proteomics @@ -21830,6 +23233,7 @@ Map peptides to a reference genome for display by a genome browser + To update Proteomics @@ -21850,6 +23254,7 @@ wrapper for MaxQuant + Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics @@ -21870,6 +23275,7 @@ MetaProteomeAnalyzer + Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics @@ -21890,6 +23296,7 @@ MetaGeneAnnotator gene-finding program for prokaryote and phage + To update Sequence Analysis @@ -21910,6 +23317,7 @@ Produce targeted databases for mass spectrometry analysis. + Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics @@ -21930,6 +23338,7 @@ quantitative analysis of microbiome taxonomy and function + Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics @@ -21950,6 +23359,7 @@ + Up-to-date @@ -21970,6 +23380,7 @@ moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. + Up-to-date https://github.com/compomics/moFF Proteomics @@ -21990,6 +23401,7 @@ Morpheus MS Search Application + To update Proteomics @@ -22010,6 +23422,7 @@ MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA + To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics @@ -22030,6 +23443,7 @@ msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container + To update Proteomics @@ -22050,6 +23464,7 @@ MSGF+ + To update Proteomics @@ -22070,6 +23485,7 @@ Extract MS/MS scans from the mzML file(s) based on PSM report. + To update Proteomics @@ -22090,6 +23506,7 @@ MSstats tool for analyzing mass spectrometry proteomic datasets + To update https://github.com/MeenaChoi/MSstats Proteomics @@ -22110,6 +23527,7 @@ MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling + To update http://msstats.org/msstatstmt/ Proteomics @@ -22130,6 +23548,7 @@ Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome + To update Proteomics @@ -22150,6 +23569,7 @@ Creates a SQLite database for proteomics data + To update Proteomics @@ -22170,6 +23590,7 @@ OpenMS Suite for LC/MS data management and analyses + To update https://www.openms.de/ Proteomics @@ -22190,6 +23611,7 @@ Reactome Pathway Matcher + To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics @@ -22210,6 +23632,7 @@ PepPointer categorizes peptides by their genomic coordinates. + To update Genomic Interval Operations, Proteomics @@ -22230,6 +23653,7 @@ A peptide-centric MS search engine for novel peptide identification and validation. + To update https://pepquery.org Proteomics @@ -22250,6 +23674,7 @@ PepQuery2 peptide-centric MS search for peptide identification and validation + Up-to-date https://pepquery.org Proteomics @@ -22270,6 +23695,7 @@ Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files + To update Proteomics @@ -22281,7 +23707,7 @@ peptideshaker - 4.3.5 + 4.3.6 searchgui To update @@ -22290,6 +23716,7 @@ PeptideShaker and SearchGUI + To update http://compomics.github.io Proteomics @@ -22310,6 +23737,7 @@ Convert PepXML to Tabular + To update Proteomics @@ -22330,6 +23758,7 @@ Percolator + Up-to-date Proteomics @@ -22350,6 +23779,7 @@ HiRIEF tools + To update Proteomics @@ -22370,6 +23800,7 @@ Calculate Precursor Mass Discrepancy (PMD) for MS/MS + To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics @@ -22390,6 +23821,7 @@ CustomProDB + To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics @@ -22410,6 +23842,7 @@ CustomProDB Annotation + To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics @@ -22430,6 +23863,7 @@ PSM to SAM + To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics @@ -22450,6 +23884,7 @@ + To update @@ -22470,6 +23905,7 @@ Retrieve cDNA features from Ensembl REST API in BED format + To update http://rest.ensembl.org/ Data Source @@ -22490,6 +23926,7 @@ Translate BED transcript CDS or cDNA in 3 frames + To update http://rest.ensembl.org/ Proteomics @@ -22510,6 +23947,7 @@ The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. + To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics @@ -22530,6 +23968,7 @@ The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. + To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics @@ -22550,6 +23989,7 @@ The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. + To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics @@ -22570,6 +24010,7 @@ The tool MzMLToMzLite allows to convert mzML files to mzLite files. + Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics @@ -22590,6 +24031,7 @@ The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. + Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics @@ -22610,6 +24052,7 @@ Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. + Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics @@ -22630,6 +24073,7 @@ MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. + Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics @@ -22650,6 +24094,7 @@ The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. + To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics @@ -22670,6 +24115,7 @@ The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. + Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics @@ -22690,6 +24136,7 @@ ProteoRE JVenn Diagram + To update Proteomics @@ -22710,6 +24157,7 @@ + To update @@ -22730,6 +24178,7 @@ + To update @@ -22750,6 +24199,7 @@ Validate PSM from Ion Fragmentation + To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics @@ -22770,6 +24220,7 @@ Semi-supervised learning and scoring of OpenSWATH results. + To update https://github.com/PyProphet/pyprophet Proteomics @@ -22781,7 +24232,7 @@ pyteomics 4.4.1 - 4.6.3 + 4.7.1 pyteomics To update pyteomics @@ -22790,6 +24241,7 @@ Proteomics, Proteomics experiment Tools using the pyteomics library Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. + To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics @@ -22810,6 +24262,7 @@ Correlation between protein and transcript abundance + To update Proteomics @@ -22830,6 +24283,7 @@ Isobaric Quantitation using QuantWiz-IQ + Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics @@ -22850,6 +24304,7 @@ Split ROI coordinates of QuPath TMA annotation by cell type + To update https://github.com/npinter/ROIsplitter Imaging @@ -22870,6 +24325,7 @@ Raw Tools + To update https://github.com/kevinkovalchik/RawTools Proteomics @@ -22890,6 +24346,7 @@ Use python regular expressions to find and replace text + To update Text Manipulation @@ -22910,6 +24367,7 @@ + To update @@ -22930,6 +24388,7 @@ Six-frame Genome-Inferred Libraries for LC-MS/MS + Up-to-date Proteomics, MetaProteomics @@ -22950,6 +24409,7 @@ Filter from spectraST files to swath input files + To update Proteomics @@ -22970,6 +24430,7 @@ Filter from spectraST files to swath input files + To update Proteomics @@ -22990,6 +24451,7 @@ Perform 3 frame translation of BED file augmented with a sequence column + To update Proteomics @@ -23010,6 +24472,7 @@ Unipept retrieves metaproteomics information + To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics @@ -23030,6 +24493,7 @@ Download UniProt proteome in XML or fasta format + To update Proteomics @@ -23050,6 +24514,7 @@ runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. + To update Fasta Manipulation, Proteomics @@ -23070,6 +24535,7 @@ Bio3d is a program that can be used to analyse molecular dynamics trajectories. + To update http://thegrantlab.org/bio3d/index.php Computational chemistry @@ -23090,6 +24556,7 @@ Tools for MD analysis + To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry @@ -23110,6 +24577,7 @@ Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. + To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry @@ -23130,6 +24598,7 @@ PACKMOL is a package for creating starting structures for Molecular Dynamics simulations + To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry @@ -23150,6 +24619,7 @@ Set of python scripts and associated tool files that can be used to modify topology files. + To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry @@ -23170,6 +24640,7 @@ Free energy tools of BRIDGE. + To update Molecular Dynamics, Computational chemistry @@ -23190,6 +24661,7 @@ GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. + To update https://github.com/gromacs Molecular Dynamics, Computational chemistry @@ -23210,6 +24682,7 @@ MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations + To update https://github.com/MDAnalysis/mdanalysis Computational chemistry @@ -23230,6 +24703,7 @@ A tool for interconverting between different MD structure and trajectory file formats. + To update Molecular Dynamics, Computational chemistry @@ -23250,6 +24724,7 @@ A tool for slicing trajectory files using MDTraj. + To update Molecular Dynamics, Computational chemistry @@ -23270,6 +24745,7 @@ MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories + To update https://github.com/mdtraj/mdtraj Computational chemistry @@ -23290,6 +24766,7 @@ OpenMM is a toolkit for molecular simulation using high performance GPU code. + To update https://github.com/openmm Molecular Dynamics, Computational chemistry @@ -23310,6 +24787,7 @@ vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations + To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry @@ -23330,6 +24808,7 @@ filter bam files before somatic-varscan or lumpy-smoove analysis + To update http://artbio.fr SAM, Variant Analysis @@ -23350,6 +24829,7 @@ Generates hit count lists from bam alignments. + To update http://artbio.fr RNA, Transcriptomics @@ -23370,6 +24850,7 @@ Converts a bigWig file to bedGraph format + To update http://artbio.fr Convert Formats @@ -23390,6 +24871,7 @@ Converts a bigWig file to Wiggle (WIG) format + To update https://artbio.fr Convert Formats @@ -23410,6 +24892,7 @@ Generate DNA scaffold from blastn or tblastx alignments of Contigs + To update http://artbio.fr RNA, Sequence Analysis, Assembly @@ -23430,6 +24913,7 @@ Extract unmatched query sequences from blast + To update http://artbio.fr Fasta Manipulation @@ -23450,6 +24934,7 @@ Parse blast outputs and compile hits + To update http://artbio.fr Assembly, RNA @@ -23470,6 +24955,7 @@ Generate DNA scaffold from blastx alignment of Contigs + To update http://artbio.fr RNA, Sequence Analysis, Assembly @@ -23490,6 +24976,7 @@ cap3 wrapper + To update http://artbio.fr Assembly @@ -23510,6 +24997,7 @@ Pick fasta sequence with specific header content + To update http://artbio.fr Fasta Manipulation @@ -23530,6 +25018,7 @@ Concatenate multiple datasets tail-to-head, including collection datasets. + To update http://artbio.fr Text Manipulation @@ -23550,6 +25039,7 @@ Generate CPM,TPM or RPK from raw counts + To update http://artbio.fr Transcriptomics @@ -23570,6 +25060,7 @@ Normalizes gene hitlists + To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics @@ -23588,14 +25079,36 @@ - Converts EMBL flat format to fasta format + Converts EMBL flat format to fasta format + + + To update + http://artbio.fr + Text Manipulation + embl2fa + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa + + + + ez_histograms + 3.4.4 + 2.2.1 + r-ggplot2 + To update + + + + + ggplot2 histograms and density plots + To update - http://artbio.fr - Text Manipulation - embl2fa + https://github.com/tidyverse/ggplot2 + Visualization, Statistics + ez_histograms artbio - https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa + https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms @@ -23610,6 +25123,7 @@ Fetch fasta sequences from NCBI using eutils wrappers + To update http://artbio.fr Fasta Manipulation, Data Source @@ -23630,6 +25144,7 @@ Fisher's exact test on two-column hit lists. + To update http://artbio.fr RNA, Statistics @@ -23641,7 +25156,7 @@ gatk4 4.1.7.0 - 4.4.0.0 + 4.5.0.0 gatk4 To update @@ -23650,6 +25165,7 @@ Find somatic variations + To update http://artbio.fr Variant Analysis @@ -23670,6 +25186,7 @@ Obtain reference genome sequence. + To update http://artbio.fr Data Source, Fasta Manipulation @@ -23690,6 +25207,7 @@ Center or scale (standardize) data + To update http://artbio.fr Statistics @@ -23710,6 +25228,7 @@ Filter single cell RNAseq data on libray depth and number of detected genes + To update http://artbio.fr Transcriptomics @@ -23730,6 +25249,7 @@ Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data + To update http://artbio.fr Transcriptomics @@ -23750,6 +25270,7 @@ Compute single-cell paire-wise gene expressions correlations + To update http://artbio.fr Transcriptomics @@ -23770,6 +25291,7 @@ Generates PCA, t-SNE and HCPC visualisation + To update http://artbio.fr Transcriptomics, Visualization @@ -23790,6 +25312,7 @@ Perform a mann-whitney differential testing between two sets of gene expression data + To update http://artbio.fr Transcriptomics @@ -23810,6 +25333,7 @@ Normalize raw counts using scran + To update http://artbio.fr Transcriptomics @@ -23830,6 +25354,7 @@ Compute signature scores from single cell RNAseq data + To update http://artbio.fr Transcriptomics @@ -23850,6 +25375,7 @@ A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies + To update http://artbio.fr Nanopore @@ -23870,6 +25396,7 @@ gplot heatmap.2 function adapted for plotting large heatmaps + To update https://github.com/cran/gplots Visualization @@ -23890,6 +25417,7 @@ Unix diff + To update http://artbio.fr Text Manipulation @@ -23910,6 +25438,7 @@ Compress fastq sequence files + To update http://artbio.fr Convert Formats @@ -23930,6 +25459,7 @@ Galaxy wrapper of the lumpy-using smoove workflow + To update http://artbio.fr Variant Analysis @@ -23941,8 +25471,8 @@ manta 1.6 - 1.19.2 - samtools + 1.6.0 + manta To update @@ -23950,6 +25480,7 @@ Structural variant and indel caller for mapped sequencing data + To update http://artbio.fr Variant Analysis @@ -23960,7 +25491,7 @@ mapping_quality_stats - 0.19.1+galaxy0 + 0.22.0 1.3.2 r-optparse To update @@ -23970,17 +25501,18 @@ Collects and shows the distribution of MAPQ values in a BAM alignment file + To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio - https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats + https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats mircounts - 1.5.1 + 1.6 tar To update @@ -23990,6 +25522,7 @@ Generates miRNA count lists from read alignments to mirBase. + To update http://artbio.fr RNA, Transcriptomics @@ -24000,27 +25533,28 @@ mutational_patterns - 3.4.0+galaxy2 + 3.12.0 3.12.0 bioconductor-mutationalpatterns - To update + Up-to-date Mutational patterns and signatures in base substitution catalogs - To update + + Up-to-date http://artbio.fr Variant Analysis mutational_patterns artbio - https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns + https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns oases - 1.3.0 + 1.4.0 0.2.09 oases To update @@ -24030,47 +25564,50 @@ Short read assembler + To update http://artbio.fr Assembly, RNA oases artbio - https://github.com/ARTbio/tools-artbio/tree/master/tools/oases + https://github.com/ARTbio/tools-artbio/tree/main/tools/oases pathifier - 1.0.2 - 1.3.2 - r-optparse - To update + 1.40.0 + 1.40.0 + bioconductor-pathifier + Up-to-date pathifier - To update + + Up-to-date https:// Transcriptomics, Statistics pathifier artbio - https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier + https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier pindel - 0.2.5b8+galaxy1 + 0.2.5b9 0.2.5b9 pindel - To update + Up-to-date Pindel detects genome-wide structural variation. - To update + + Up-to-date http://artbio.fr Variant Analysis pindel @@ -24080,22 +25617,23 @@ probecoverage - 0.7.0 - 1.19.2 - samtools - To update + 0.22.0 + 0.22.0 + pysam + Up-to-date computes and plots read coverage of genomic regions by sequencing datasets - To update + + Up-to-date http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio - https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage + https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage @@ -24110,6 +25648,7 @@ Repeat element profiling + To update https://github.com/nskvir/RepEnrich Transcriptomics, Variant Analysis @@ -24130,6 +25669,7 @@ transcript quantification from RNA-Seq data + To update https://github.com/deweylab/RSEM Transcriptomics, RNA @@ -24150,6 +25690,7 @@ filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM + To update http://artbio.fr SAM @@ -24170,6 +25711,7 @@ Generates a sashimi plot from bam files. + To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization @@ -24190,6 +25732,7 @@ various fasta to tabular conversions + To update http://artbio.fr Convert Formats, Fasta Manipulation @@ -24210,6 +25753,7 @@ clusters small rna reads in alignment BAM files + To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers @@ -24230,6 +25774,7 @@ Generates small read maps from alignment BAM files + To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers @@ -24250,6 +25795,7 @@ Computes the tendency of small RNAs to overlap with each other. + To update http://artbio.fr RNA @@ -24270,6 +25816,7 @@ infer copy number variations from a vcf file with SNVs using R sequenza + To update http://artbio.fr Variant Analysis @@ -24290,6 +25837,7 @@ bowtie wrapper tool to align small RNA sequencing reads + To update http://artbio.fr RNA, Next Gen Mappers @@ -24310,6 +25858,7 @@ Maps iteratively small RNA sequencing datasets to reference sequences. + To update http://artbio.fr RNA @@ -24330,6 +25879,7 @@ produces a tar.gz archive of fast5 sequence files + To update http://artbio.fr Nanopore @@ -24350,6 +25900,7 @@ Compute variant allele frequency in vcf files generated by varscan. + To update http://artbio.fr Variant Analysis @@ -24370,6 +25921,7 @@ Identification and quantification of differential RNA modifications from direct RNA sequencing + To update https://github.com/GoekeLab/xpore Nanopore @@ -24390,6 +25942,7 @@ Clips 3' adapters for small RNA sequencing reads. + To update http://artbio.fr RNA, Fastq Manipulation @@ -24410,6 +25963,7 @@ Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa + To update https://github.com/EDIorg/EMLassemblyline Ecology @@ -24430,6 +25984,7 @@ Tools to compute ecoregionalization with BRT model predictions and clustering. + To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology @@ -24450,6 +26005,7 @@ Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). + To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology @@ -24470,6 +26026,7 @@ Tools to compute and analyse biodiversity metrics + To update Ecology @@ -24490,6 +26047,7 @@ Tool to convert ab1 files into FASTQ files + To update Convert Formats @@ -24510,6 +26068,7 @@ Compute indicators for turnover boulders fields + To update Ecology @@ -24530,6 +26089,7 @@ Tool to compute a consensus sequence from several aligned fasta sequences + To update Sequence Analysis @@ -24550,6 +26110,7 @@ Explore data through multiple statistical tools + To update Ecology @@ -24570,6 +26131,7 @@ xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. + To update http://xarray.pydata.org Ecology @@ -24590,6 +26152,7 @@ Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. + To update https://www.gdal.org Ecology @@ -24610,6 +26173,7 @@ Run IDW interpolation based on a .csv and .geojson file + To update https://github.com/AquaINFRA/galaxy Ecology @@ -24617,6 +26181,27 @@ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation + + + medenv + 0.0.1 + + pandas + To update + + + + + Retrieve environmental data from etopo, cmems and woa + + + To update + https://github.com/jeremyfix/medenv + Ecology, Data Source + + ecology + https://github.com/jeremyfix/medenv + obisindicators @@ -24630,6 +26215,7 @@ Compute biodiveristy indicators for marine data from obis + To update https://github.com/Marie59/obisindicators Ecology @@ -24650,6 +26236,7 @@ Access, process, visualise oceanographic data for the Earth System + To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology @@ -24670,6 +26257,7 @@ + To update https://github.com/RetoSchmucki/regionalGAM Ecology @@ -24690,6 +26278,7 @@ Get species occurences data + To update https://cran.r-project.org/web/packages/spocc/index.html Ecology @@ -24710,6 +26299,7 @@ Compute biodiversity indicators for remote sensing data from Sentinel 2 + To update Ecology @@ -24730,6 +26320,7 @@ Tools to analyse STOC data. + To update Ecology @@ -24750,6 +26341,7 @@ Tools created by the vigiechiro team to analyses and identify chiro sounds files. + To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology @@ -24770,6 +26362,7 @@ Tool to convert a xml file from one metadata standard to another + To update Convert Formats @@ -24780,7 +26373,7 @@ c3s - 0.1.0 + 0.2.0 python To update @@ -24790,6 +26383,7 @@ Copernicus Climate Change Service (C3S) + To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis @@ -24810,6 +26404,7 @@ Copernicus Atmosphere Data Store (ADS) + To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis @@ -24830,6 +26425,7 @@ CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. + To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis @@ -24850,6 +26446,7 @@ Community Earth System Model (CESM) + Up-to-date https://www.cesm.ucar.edu/ Climate Analysis @@ -24870,6 +26467,7 @@ Create climate stripes from a tabular input file + To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization @@ -24890,6 +26488,7 @@ Earth Observation Data Information Extractor + To update https://eodie.readthedocs.io/ Climate Analysis @@ -24910,6 +26509,7 @@ Get Copernicus Essential Climate Variables for assessing climate variability + To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source @@ -24930,6 +26530,7 @@ EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model + To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis @@ -24950,6 +26551,7 @@ Creates a png image showing statistic over areas as defined in the vector file + To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis @@ -24970,6 +26572,7 @@ Visualization of regular geographical data on a map with psyplot + To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis @@ -24990,6 +26593,7 @@ Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees + To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis @@ -25010,6 +26614,7 @@ Retrieve data from Volcanoes of the World (VOTW) Database + To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data @@ -25030,6 +26635,7 @@ Make a cell barcode plot for droplet single-cell RNA-seq QC + To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis @@ -25050,6 +26656,7 @@ Retrieval and download of FASTQ files from ENA and other repositories such as HCA. + To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics @@ -25070,6 +26677,7 @@ Utility to extract annotations from Ensembl GTF files. + To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis @@ -25090,6 +26698,7 @@ Paired-end fastq pairer + To update https://github.com/linsalrob/fastq-pair Fastq Manipulation @@ -25110,6 +26719,7 @@ FASTQ trimmer based on quality + To update https://github.com/agordon/fastx_toolkit Fastq Manipulation @@ -25130,6 +26740,7 @@ Set of tools for handling fastq files + To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA @@ -25150,6 +26761,7 @@ Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data + To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis @@ -25170,6 +26782,7 @@ Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis + To update Transcriptomics, RNA, Statistics @@ -25190,6 +26803,7 @@ Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects + To update Transcriptomics, Sequence Analysis @@ -25210,6 +26824,7 @@ Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home + To update Transcriptomics, Sequence Analysis @@ -25230,6 +26845,7 @@ decoupler - Ensemble of methods to infer biological activities + To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics @@ -25250,6 +26866,7 @@ De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25270,6 +26887,7 @@ De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25290,6 +26908,7 @@ De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25310,6 +26929,7 @@ De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25320,8 +26940,8 @@ scanpy - 1.8.1 - 1.1.6 + 1.9.3 + 1.9.301 scanpy-scripts To update @@ -25330,6 +26950,7 @@ scanpy-scripts, command-line wrapper scripts around Scanpy. + To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA @@ -25350,6 +26971,7 @@ De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25370,6 +26992,7 @@ SCCAF: Single Cell Clustering Assessment Framework. + To update https://github.com/sccaf/sccaf Transcriptomics @@ -25390,6 +27013,7 @@ Convert scRNA data object between popular formats + To update Transcriptomics @@ -25410,6 +27034,7 @@ De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25430,6 +27055,7 @@ De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 + To update Transcriptomics, RNA, Statistics, Sequence Analysis @@ -25440,28 +27066,29 @@ seurat - 0.3.0 + 4.0.0 4.0.0 seurat-scripts - To update + Up-to-date De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 - To update + Up-to-date + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa - https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + ucsc-cell-browser 1.0.0+galaxy1 - 1.2.3 + 1.2.5 ucsc-cell-browser To update @@ -25470,6 +27097,7 @@ Python pipeline and Javascript scatter plot library for single-cell datasets + To update https://cells.ucsc.edu/ Transcriptomics @@ -25490,6 +27118,7 @@ Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR BioTransformer is a tool for prediction of small molecule metabolism in mammals. BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. + Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics @@ -25510,6 +27139,7 @@ Tool for filtering organometallics/anorganic compounds from a list of compounds. + To update https://github.com/RECETOX/galaxytools/ Metabolomics @@ -25521,7 +27151,7 @@ matchms 0.24.0 - 0.24.1 + 0.24.2 matchms To update matchms @@ -25530,6 +27160,7 @@ Metabolomics Searching, filtering and converting mass spectral libraries. Tool to import, process, clean, and compare mass spectrometry data. + To update https://github.com/matchms/matchms Metabolomics @@ -25537,6 +27168,27 @@ recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms + + + misc + 1.0.0 + + + To update + + + + + + + + To update + https://github.com/RECETOX/galaxytools + Metabolomics + + recetox + https://github.com/RECETOX/galaxytools/tree/master/tools/misc + msmetaenhancer @@ -25550,6 +27202,7 @@ Metabolomics, Compound libraries and screening, Data submission, annotation and curation Tool for mass spectra metadata annotation. + Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics @@ -25561,7 +27214,7 @@ msp_merge 0.1.0 - 0.24.1 + 0.24.2 matchms To update @@ -25570,6 +27223,7 @@ + To update https://github.com/RECETOX/galaxytools Metabolomics @@ -25590,6 +27244,7 @@ mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. + To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics @@ -25597,6 +27252,27 @@ recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator + + + qcxms + 5.2.1 + + + To update + + + + + QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). + + + To update + https://github.com/grimme-lab/QCxMS + Computational chemistry, Molecular Dynamics + QCxMS + recetox + https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms + query @@ -25610,6 +27286,7 @@ Execute an SQL statement on a set of tables + To update Text Manipulation @@ -25630,6 +27307,7 @@ Metabolomics A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. + To update https://rdrr.io/cran/RAMClustR/ Metabolomics @@ -25650,6 +27328,7 @@ Metabolomics Peak detection tool for HRMS profile data. recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. + Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics @@ -25670,6 +27349,7 @@ Metabolomics This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. + To update https://github.com/RECETOX/recetox-msfinder Metabolomics @@ -25690,6 +27370,7 @@ Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. + Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics @@ -25710,6 +27391,7 @@ Removes molecular coordination complexes. + To update https://github.com/RECETOX/galaxytools Metabolomics @@ -25730,6 +27412,7 @@ Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. + To update https://github.com/PaoloBnn/Retip Metabolomics @@ -25740,8 +27423,8 @@ riassigner - 0.3.4 - 0.3.4 + 0.4.0 + 0.4.0 riassigner Up-to-date riassigner @@ -25750,6 +27433,7 @@ Metabolomics, Compound libraries and screening, Data submission, annotation and curation RIAssigner is a python tool for retention index (RI) computation for GC-MS data. + Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics @@ -25770,6 +27454,7 @@ RMassBank is an R package for processing tandem MS files and building of MassBank records. + To update https://github.com/MassBank/RMassBank Metabolomics @@ -25790,6 +27475,7 @@ Proteomics experiment, Metabolomics, Natural language processing, Proteomics Mass spectra similarity scoring using a trained Spec2Vec model. Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. + Up-to-date https://github.com/iomega/spec2vec Metabolomics @@ -25810,6 +27496,7 @@ Metabolomics Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. + Up-to-date https://github.com/RECETOX/WaveICA Metabolomics @@ -25830,6 +27517,7 @@ Performs semiempirical molecular optimization. + To update https://github.com/grimme-lab/xtb Metabolomics @@ -25850,6 +27538,7 @@ Combines freebayes and mpileup files for use by vcf2snvalignment + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -25870,6 +27559,7 @@ Filter out position based on distance between SNVs + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -25890,6 +27580,7 @@ SNVPhyl filter_stats + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -25910,6 +27601,7 @@ SNVPhyl filter_vcf + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -25930,6 +27622,7 @@ Find repetitive regions on a reference genome using MUMMer + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -25950,6 +27643,7 @@ Generate alignment of SNVs from SNVPhyl variant table. + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis @@ -25970,6 +27664,7 @@ Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis @@ -25990,6 +27685,7 @@ Generate matrix of SNV distances + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -26010,6 +27706,7 @@ Generates multiple alignment of variant calls + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -26030,6 +27727,7 @@ Checks the mapping quality of all BAM(s) + Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis @@ -26050,6 +27748,7 @@ SNVPhyl suite defining all dependencies for SNVPhyl + To update Sequence Analysis @@ -26070,6 +27769,7 @@ cooler different tools to process Hi-C from mirnylab + To update https://github.com/open2c/cooler Epigenetics @@ -26090,6 +27790,7 @@ Convert the output of hicup (as sam or bam) to the input of juicebox. + To update Epigenetics @@ -26110,6 +27811,7 @@ Convert GTF files to BED12 format + To update https://pythonhosted.org/gffutils/contents.html Convert Formats @@ -26130,6 +27832,7 @@ Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension + To update Epigenetics @@ -26150,6 +27853,7 @@ Generate blach corrected movie from hyperstack + To update Imaging @@ -26170,6 +27874,7 @@ Combine images to stack and upload to the omero server + To update Imaging @@ -26190,6 +27895,7 @@ Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index + To update Imaging @@ -26210,6 +27916,7 @@ Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down + To update Imaging @@ -26230,6 +27937,7 @@ Get omero id of children of an omero object id + To update Imaging @@ -26250,6 +27958,7 @@ Analyse Hyperstack on OMERO server to measure fluorescence levels + To update Imaging @@ -26260,7 +27969,7 @@ omero_hyperstack_to_gastruloid_measurements - 20231220 + 20240214 20231211 fiji To update @@ -26270,6 +27979,7 @@ Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements + To update Imaging @@ -26290,6 +28000,7 @@ Revert the mapped orientation of R2 mates in a bam. + To update SAM @@ -26310,6 +28021,7 @@ Upload the ROI coordinates and the measurements to the omero server + To update Imaging @@ -26330,6 +28042,7 @@ Maps BLAST results to GO annotation terms + To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis @@ -26350,6 +28063,7 @@ BLAST Reciprocal Best Hits (RBH) from two FASTA files + To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis @@ -26370,6 +28084,7 @@ Make table of top BLAST match descriptions + To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation @@ -26390,6 +28105,7 @@ Make a FASTA file non-redundant + To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis @@ -26410,6 +28126,7 @@ NCBI BLAST+ + To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html index 0c96dc24..cb16700f 100644 --- a/results/microgalaxy/index.html +++ b/results/microgalaxy/index.html @@ -58,97 +58,108 @@ Expand Galaxy wrapper id - Galaxy wrapper version - Conda version - Conda id - Status + Total tool usage (usegalaxy.eu) + No. of tool users (2022-2023) (usegalaxy.eu) + Galaxy tool ids + Description bio.tool id + bio.tool ids + biii bio.tool name + bio.tool description EDAM operation EDAM topic - Description - bio.tool description Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source + Galaxy wrapper parsed folder + Galaxy wrapper version + Conda id + Conda version + https://usegalaxy.org + https://usegalaxy.org.au + https://usegalaxy.eu + https://usegalaxy.fr + Deprecated - TreeBest - 1.9.2.post0 - 1.9.2.post1 - treebest - To update + PAMPA + + + pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm + Tools to compute and analyse biodiversity metrics + - TreeBeST best - To update - http://treesoft.sourceforge.net/treebest.shtml - Phylogenetics - treebest_best - earlhaminst - https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest - - - ete - 3.1.2 - 3.1.1 - ete3 To update + Ecology + pampa + ecology + https://github.com/ColineRoyaux/PAMPA-Galaxy + https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA + 0.0.2 + + (0/5) + (5/5) + (5/5) + (5/5) + False + + + TreeBest - Analyse phylogenetic trees using the ETE Toolkit + treebest_best + TreeBeST best + treebest + treebest + + TreeBeST + TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. + Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) + Phylogenetics To update - http://etetoolkit.org/ + http://treesoft.sourceforge.net/treebest.shtml Phylogenetics - ete + treebest_best earlhaminst - https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest + 1.9.2.post0 + treebest + 1.9.2.post1 + (0/1) + (0/1) + (1/1) + (0/1) + False - lotus2 - 2.32 - 2.32 - lotus2 - Up-to-date - lotus2 - lotus2 - Sequence feature detection - Metagenomics - LotuS2 OTU processing pipeline - LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. - Up-to-date - http://lotus2.earlham.ac.uk/ - Metagenomics - lotus2 - earlhaminst - https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 - - + abacas + abacas - 1.1 - 3.23 - mummer - To update + Order and Orientate Contigs + + - Order and Orientate Contigs To update https://github.com/phac-nml/abacas @@ -156,2419 +167,3569 @@ abacas nml https://github.com/phac-nml/abacas + https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas + 1.1 + mummer + 3.23 + (0/1) + (0/1) + (0/1) + (1/1) + False - assemblystats - 1.1.0 - 1.7.8 - perl-bioperl - To update - - - - - Summarise an assembly (e.g. N50 metrics) + abricate + 496717.0 + 1764.0 + abricate, abricate_list, abricate_summary + Mass screening of contigs for antiobiotic resistance genes + ABRicate + ABRicate - To update - https://github.com/phac-nml/galaxy_tools - Assembly - assemblystats - nml - https://github.com/phac-nml/galaxy_tools + ABRicate + Mass screening of contigs for antimicrobial resistance or virulence genes. + Antimicrobial resistance prediction + Genomics, Microbiology + Up-to-date + https://github.com/tseemann/abricate + Sequence Analysis + abricate + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate + 1.0.1 + abricate + 1.0.1 + (3/3) + (3/3) + (3/3) + (3/3) + False - biohansel - 2.4.0 - 2.6.1 - bio_hansel - To update - - + abritamr - Heidelberg and Enteritidis SNP Elucidation + abritamr + A pipeline for running AMRfinderPlus and collating results into functional classes + abritamr + abritamr + abriTAMR + an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. + Antimicrobial resistance prediction + Microbiology, Public health and epidemiology, Infectious disease To update - https://github.com/phac-nml/biohansel + https://zenodo.org/record/7370628 Sequence Analysis - biohansel - nml - https://github.com/phac-nml/biohansel + abritamr + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr + https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr + 1.0.14 + abritamr + 1.0.17 + (0/1) + (0/1) + (1/1) + (0/1) + False - combine_assembly_stats - 1.0 - 2.54 - perl-getopt-long - To update - - + abyss + 4278.0 + 391.0 + abyss-pe + Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler + abyss + abyss + ABySS + De novo genome sequence assembler using short reads. + Genome assembly, De-novo assembly, Scaffolding + Sequence assembly + Up-to-date + http://www.bcgsc.ca/platform/bioinfo/software/abyss + Assembly + abyss + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss + https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss + 2.3.7 + abyss + 2.3.7 + (0/1) + (1/1) + (1/1) + (0/1) + False + + - Combine multiple Assemblystats datasets into a single tabular report + aldex2 + 129.0 + 13.0 + aldex2 + Performs analysis Of differential abundance taking sample variation into account + aldex2 + aldex2 + ALDEx2 + A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. + Statistical inference + Gene expression, Statistics and probability To update - https://github.com/phac-nml/galaxy_tools - Assembly - combine_assemblystats - nml - https://github.com/phac-nml/galaxy_tools + https://github.com/ggloor/ALDEx_bioc + Metagenomics + aldex2 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 + 1.26.0 + bioconductor-aldex2 + 1.34.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - cryptogenotyper - 1.0 - 1.0 - cryptogenotyper - Up-to-date - + amplican + 53.0 + 12.0 + amplican + AmpliCan is an analysis tool for genome editing. + amplican + amplican + amplican + It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. + Alignment, Standardisation and normalisation + PCR experiment, Statistics and probability + To update + https://github.com/valenlab/amplican + Sequence Analysis + amplican + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican + https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican + 1.14.0 + bioconductor-amplican + 1.24.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + amrfinderplus + 591.0 - CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. + amrfinderplus + "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. + amrfinderplus + amrfinderplus + AMRFinderPlus + AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms + Antimicrobial resistance prediction + Microbiology, Public health and epidemiology, Infectious disease Up-to-date - https://github.com/phac-nml/CryptoGenotyper + https://github.com/ncbi/amr Sequence Analysis - cryptogenotyper - nml - https://github.com/phac-nml/CryptoGenotyper + AMRFinderPlus + iuc + https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus + https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus + 3.12.8 + ncbi-amrfinderplus + 3.12.8 + (0/1) + (0/1) + (1/1) + (1/1) + False - ectyper - 1.0.0 - 1.0.0 - ectyper - Up-to-date - - + ancombc + 7.0 + 4.0 + ancombc + Performs analysis of compositions of microbiomes with bias correction. + ancombc + ancombc + ANCOMBC + Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. + DNA barcoding + Microbial ecology, Metagenomics, Taxonomy + To update + https://github.com/FrederickHuangLin/ANCOMBC + Metagenomics + ancombc + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc + 1.4.0 + bioconductor-ancombc + 2.4.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + - EC-Typer - in silico serotyping of Escherichia coli species + antismash + 14596.0 + 279.0 + antismash + Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters + antismash + antismash - Up-to-date - https://github.com/phac-nml/ecoli_serotyping + antiSMASH + Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. + Sequence clustering, Gene prediction, Differential gene expression analysis + Molecular interactions, pathways and networks, Gene and protein families + To update + https://antismash.secondarymetabolites.org Sequence Analysis - ectyper - nml - https://github.com/phac-nml/ecoli_serotyping + antismash + bgruening + https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash + https://github.com/bgruening/galaxytools/tree/master/tools/antismash + 6.1.1 + antismash + 7.1.0 + (1/1) + (1/1) + (1/1) + (0/1) + False - filter_spades_repeats - 1.0.1 - 1.7.8 - perl-bioperl - To update + artic + artic_guppyplex, artic_minion + The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building + artic + artic + ARTIC + A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + Sequence alignment + Genomics + To update + https://github.com/artic-network/fieldbioinformatics + Sequence Analysis - Remove short and repeat contigs/scaffolds + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic + https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic - To update - https://github.com/phac-nml/galaxy_tools/ - Assembly - filter_spades_repeats - nml - https://github.com/phac-nml/galaxy_tools/ + artic + 1.2.4 + (0/2) + (0/2) + (2/2) + (0/2) + False - getmlst - 0.1.4.1 - 0.2.0 - srst2 - To update - - - - - Download MLST datasets by species from pubmlst.org + assemblystats - To update - Sequence Analysis - getmlst - nml + assemblystats + Summarise an assembly (e.g. N50 metrics) - - - hivtrace - 1.0.1 - 1.5.0 - hivtrace - To update - An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update + https://github.com/phac-nml/galaxy_tools + Assembly + assemblystats + nml + https://github.com/phac-nml/galaxy_tools + https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats + 1.1.0 + perl-bioperl + 1.7.8 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + bakta + 2982.0 + 151.0 + bakta + "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." + bakta + bakta + Bakta + Rapid & standardized annotation of bacterial genomes, MAGs & plasmids + Genome annotation + Genomics, Data submission, annotation and curation, Sequence analysis + Up-to-date + https://github.com/oschwengers/bakta Sequence Analysis - hivtrace - nml - https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace + bakta + iuc + https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta + 1.9.3 + bakta + 1.9.3 + (0/1) + (1/1) + (1/1) + (1/1) + False - kat_filter - 2.3 - 2.4.2 - kat - To update + bamtools + 14039.0 + 208.0 + bamtools + Operate on and transform BAM datasets in various ways using bamtools + bamtools + bamtools + BamTools + BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. + Data handling, Sequence alignment analysis + Sequencing, Data management, Sequence analysis + Up-to-date + https://github.com/pezmaster31/bamtools + Sequence Analysis, SAM + bamtools + devteam + https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools + https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools + 2.5.2 + bamtools + 2.5.2 + (1/1) + (0/1) + (1/1) + (1/1) + False + + + bandage + 44390.0 + 2016.0 + bandage_image, bandage_info + Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily + bandage + bandage + Bandage + GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. + Sequence assembly visualisation + Genomics, Sequence assembly + Up-to-date + https://github.com/rrwick/Bandage + Visualization + bandage + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage + 2022.09 + bandage_ng + 2022.09 + (2/2) + (2/2) + (2/2) + (2/2) + False + + - Filtering kmers or reads from a database of kmers hashes + bayescan + 64.0 + 8.0 + BayeScan + Detecting natural selection from population-based genetic data + bayescan + bayescan + BayeScan + BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. + Statistical inference + Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update - + http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis - kat_filter - nml - + bayescan + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan + 2.1 + bayescan + 2.0.1 + (0/1) + (0/1) + (1/1) + (0/1) + False - mob_suite - 3.0.3 - 3.1.8 - mob_suite - To update - - + bbtools - MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies + bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole + BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. + bbmap + bbmap, bbtools - To update - https://github.com/phac-nml/mob-suite + BBMap + BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. + RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment + Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq + Up-to-date + https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis - mob_suite - nml - https://github.com/phac-nml/mob-suite + bbtools + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools + 39.06 + bbmap + 39.06 + (6/6) + (1/6) + (5/6) + (0/6) + False - mrbayes - 1.0.2 - 3.2.7 - mrbayes - To update - + bigscape + bigscape + Construct sequence similarity networks of BGCs and groups them into GCF + BiG-SCAPE + BiG-SCAPE - A program for the Bayesian estimation of phylogeny. - - To update + BiG-SCAPE + A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. + Clustering, Global alignment, Fold recognition + Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families + Up-to-date + https://github.com/medema-group/BiG-SCAPE + Metagenomics + bigscape + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape + 1.1.9 + bigscape + 1.1.9 + (0/1) + (0/1) + (1/1) + (0/1) + False + + - Sequence Analysis - mrbayes - nml + binning_refiner + 81.0 + 21.0 + bin_refiner + Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. + binning_refiner + binning_refiner + Binning_refiner + Improving genome bins through the combination of different binning programs + Read binning, Sequence clustering + Metagenomics, Sequence assembly, Microbial ecology + Up-to-date + https://github.com/songweizhi/Binning_refiner + Metagenomics + binning_refiner + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner + 1.4.3 + binning_refiner + 1.4.3 + (0/1) + (0/1) + (1/1) + (0/1) + False - mykrobe_parser - 0.1.4.1 + biohansel + + + biohansel + Heidelberg and Enteritidis SNP Elucidation + - r-base - To update - RScript to parse the results of mykrobe predictor. To update - https://github.com/phac-nml/mykrobe-parser + https://github.com/phac-nml/biohansel Sequence Analysis - mykrobe_parser + biohansel nml - https://github.com/phac-nml/mykrobe-parser + https://github.com/phac-nml/biohansel + https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel + 2.4.0 + bio_hansel + 2.6.1 + (0/1) + (0/1) + (0/1) + (0/1) + False - plasmidspades - 1.1 - 3.15.5 - spades - To update - + biom_format + biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table + The biom-format package provides a command line interface and Python API for working with BIOM files. + biomformat + biomformat - Genome assembler for assemblying plasmid - + biomformat + This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. + Formatting + Laboratory information management, Sequence analysis To update + https://github.com/biocore/biom-format + Metagenomics - Assembly - plasmidspades - nml - + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format + https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format + 2.1.15 + biom-format + 2.1.7 + (2/6) + (2/6) + (6/6) + (0/6) + False - promer - 1.2 - - python - To update - - + biotradis - Aligns two sets of contigs and reports amino acid substitutions between them + bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites + Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. + biotradis + biotradis - To update - https://github.com/phac-nml/promer - Assembly - promer - nml - https://github.com/phac-nml/promer + biotradis + The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. + Sequence analysis + Mobile genetic elements, Workflows + Up-to-date + https://www.sanger.ac.uk/science/tools/bio-tradis + Genome annotation + biotradis + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis + https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis + 1.4.5 + biotradis + 1.4.5 + (3/3) + (0/3) + (0/3) + (0/3) + False - sistr_cmd - 1.1.1 - 1.1.1 - sistr_cmd - Up-to-date - - - - - SISTR in silico serotyping tool + blast2go + 1232.0 + 101.0 + blast2go + Maps BLAST results to GO annotation terms - Up-to-date - https://github.com/phac-nml/sistr_cmd - Sequence Analysis - sistr_cmd - nml - - - smalt - 0.7.6 - 0.7.6 - smalt - Up-to-date - SMALT aligns DNA sequencing reads with a reference genome. + To update + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go + Ontology Manipulation, Sequence Analysis + blast2go + peterjc + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go + 0.0.11 + b2g4pipe - Up-to-date - http://www.sanger.ac.uk/science/tools/smalt-0 - Sequence Analysis - smalt - nml - https://sourceforge.net/projects/smalt/ + (0/1) + (0/1) + (0/1) + (0/1) + False - srst2 - 0.3.7 - 0.2.0 - srst2 - To update + blast_rbh + 22499.0 + 121.0 + blast_reciprocal_best_hits + BLAST Reciprocal Best Hits (RBH) from two FASTA files - Short Read Sequence Typing for Bacterial Pathogens - To update - Sequence Analysis - srst2 - nml + To update + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh + Fasta Manipulation, Sequence Analysis + blast_rbh + peterjc + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh + https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh + 0.3.0 + biopython + 1.70 + (0/1) + (0/1) + (1/1) + (0/1) + False - staramr - 0.10.0 - 0.10.0 - staramr - Up-to-date + blastxml_to_top_descr + 264558.0 + 159.0 + blastxml_to_top_descr + Make table of top BLAST match descriptions + - Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. - Up-to-date - https://github.com/phac-nml/staramr - Sequence Analysis - staramr - nml - https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr - - - stringmlst - 1.1.0 - 0.6.3 - stringMLST To update + https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr + Convert Formats, Sequence Analysis, Text Manipulation + blastxml_to_top_descr + peterjc + https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr + https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr + 0.1.2 + python + (0/1) + (0/1) + (1/1) + (0/1) + False + + + bracken + 18351.0 + 326.0 + est_abundance + Bayesian Reestimation of Abundance with KrakEN + bracken + bracken + Bracken + Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + Statistical calculation + Metagenomics, Microbial ecology + Up-to-date + https://ccb.jhu.edu/software/bracken/ + Sequence Analysis, Metagenomics + bracken + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken + https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken + 2.9 + bracken + 2.9 + (1/1) + (1/1) + (1/1) + (1/1) + False + + - Rapid and accurate identification of the sequence type (ST) + busco + 86180.0 + 1804.0 + busco + BUSCO assess genome and annotation completeness + busco + busco + BUSCO + Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly + Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update - + https://gitlab.com/ezlab/busco/-/releases Sequence Analysis - stringmlst - nml - + busco + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco + 5.5.0 + busco + 5.7.1 + (1/1) + (1/1) + (1/1) + (1/1) + False - repeatexplorer2 - 2.3.8 - - - To update - - + cat - Tool for annotation of repeats from unassembled shotgun reads. + cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise + Contig Annotation Tool (CAT) + cat_bins + cat_bins + CAT and BAT + Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. + Taxonomic classification, Sequence assembly, Coding region prediction + Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update - https://github.com/repeatexplorer/repex_tarean - Genome annotation - repeatexplorer2 - gga - https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 + https://github.com/dutilh/CAT + Metagenomics + contig_annotation_tool + iuc + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat + 5.2.3 + cat + 5.3 + (5/5) + (2/5) + (5/5) + (0/5) + False cd_hit_dup - 0.0.1 - 4.8.1 - cd-hit-auxtools - To update - - - - - simple tool for removing duplicates from sequencing reads - To update - Metagenomics, Sequence Analysis cd_hit_dup - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup - - + simple tool for removing duplicates from sequencing reads - multispecies_orthologous_microsats - 1.0.0 - bx-sputnik - To update - Extract orthologous microsatellites To update - Sequence Analysis, Variant Analysis - multispecies_orthologous_microsats + Metagenomics, Sequence Analysis + cd_hit_dup devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats + https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup + https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup + 0.0.1 + cd-hit-auxtools + 4.8.1 + (1/1) + (0/1) + (0/1) + (0/1) + False - quality_filter - 1.0.1 - 0.10.0 - bx-python - To update - - - - - Filter nucleotides based on quality scores - - To update + cdhit + 8278.0 + 6.0 + cd_hit + Cluster or compare biological sequence datasets + cd-hit + cd-hit - Sequence Analysis, Variant Analysis - quality_filter - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter + cd-hit + Cluster a nucleotide dataset into representative sequences. + Sequence clustering + Sequencing + Up-to-date + http://weizhongli-lab.org/cd-hit/ + Sequence Analysis, Fasta Manipulation + cd_hit + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit + 4.8.1 + cd-hit + 4.8.1 + (0/1) + (0/1) + (1/1) + (1/1) + False - gi2taxonomy - 1.1.1 - 0.9.0 - taxonomy - To update + cemitool + 98.0 + 9.0 + cemitool + Gene co-expression network analysis tool + cemitool + cemitool + CEMiTool + It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + Enrichment analysis, Pathway or network analysis + Gene expression, Transcriptomics, Microarray experiment + To update + https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html + Transcriptomics, RNA, Statistics + cemitool + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool + 1.18.1 + bioconductor-cemitool + 1.26.0 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + checkm - Fetch taxonomic representation + checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa + Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes + checkm + checkm + CheckM + CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation + Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update - https://bitbucket.org/natefoo/taxonomy + https://github.com/Ecogenomics/CheckM Metagenomics - gi2taxonomy - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy + checkm + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm + https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm + 1.2.0 + checkm-genome + 1.2.2 + (0/10) + (0/10) + (10/10) + (10/10) + False - kraken2tax - 1.2+galaxy0 + clair3 + 1856.0 + 68.0 + clair3 + Symphonizing pileup and full-alignment for high-performance long-read variant calling + clair3 + clair3 - gawk + Clair3 + Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. + Variant calling + Molecular genetics To update + https://github.com/HKU-BAL/Clair3 + Sequence Analysis, Variant Analysis + clair3 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 + 0.1.12 + clair3 + 1.0.8 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + clinod + clinod + NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins + clinod + clinod - Convert Kraken output to Galaxy taxonomy data. - + clinod + The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. + Nucleic acid sequence analysis + Sequence analysis To update - https://bitbucket.org/natefoo/taxonomy - Metagenomics - kraken2tax - devteam - https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ + http://www.compbio.dundee.ac.uk/www-nod/ + Sequence Analysis + clinod + peterjc + https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod + https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod + 0.1.0 + clinod + 1.3 + (1/1) + (0/1) + (0/1) + (0/1) + False - lca_wrapper - 1.0.1 - 0.9.0 - taxonomy - To update - - + clustalw + 46793.0 + 651.0 + clustalw + ClustalW multiple sequence alignment program for DNA or proteins + clustal2 + clustal2 + Clustal 2 (Clustal W, Clustal X) + Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. + Multiple sequence alignment + Phylogeny, Sequence analysis + Up-to-date + http://www.clustal.org/clustal2/ + Phylogenetics, Sequence Analysis + clustalw + devteam + https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw + https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw + 2.1 + clustalw + 2.1 + (1/1) + (1/1) + (1/1) + (1/1) + False + + - Find lowest diagnostic rank + cmsearch_deoverlap + 102.0 + 1.0 + cmsearch_deoverlap + removes lower scoring overlaps from cmsearch results. + cmsearch-deoverlap + cmsearch-deoverlap + cmsearch-deoverlap + Removes lower scoring overlaps from cmsearch results. + Comparison, Alignment + Biology, Medicine To update - https://bitbucket.org/natefoo/taxonomy - Metagenomics - lca_wrapper - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper + https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl + RNA + cmsearch_deoverlap + rnateam + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap + 0.08+galaxy2 + perl + + (0/1) + (0/1) + (1/1) + (0/1) + False - t2ps - 1.0.0 - 0.9.0 - taxonomy + codeml + 60901.0 + 29.0 + codeml + Detects positive selection + paml + paml + + PAML + Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. + Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis + Phylogenetics, Sequence analysis To update + http://abacus.gene.ucl.ac.uk/software/paml.html + Phylogenetics + codeml + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml + https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml + 4.9 + paml + 4.10.7 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + cojac + cooc_mutbamscan, cooc_pubmut, cooc_tabmut + co-occurrence of mutations on amplicons + cojac + cojac - Draw phylogeny + COJAC + CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. - To update - https://bitbucket.org/natefoo/taxonomy - Metagenomics - t2ps - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps + Genetic variation + Up-to-date + https://github.com/cbg-ethz/cojac + Metagenomics, Sequence Analysis + cojac + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac + 0.9.1 + cojac + 0.9.1 + (2/3) + (0/3) + (3/3) + (0/3) + False - t2t_report - 1.0.0 - 0.9.0 - taxonomy - To update + combine_assembly_stats + combine_stats + Combine multiple Assemblystats datasets into a single tabular report - Summarize taxonomy - To update - https://bitbucket.org/natefoo/taxonomy - Metagenomics - t2t_report - devteam - https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report - - - antismash - 6.1.1 - 6.1.1 - antismash - Up-to-date - antismash - antiSMASH - Sequence clustering, Gene prediction, Differential gene expression analysis - Molecular interactions, pathways and networks, Gene and protein families - Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters - Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. - Up-to-date - https://antismash.secondarymetabolites.org - Sequence Analysis - antismash - bgruening - https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash + + + + To update + https://github.com/phac-nml/galaxy_tools + Assembly + combine_assemblystats + nml + https://github.com/phac-nml/galaxy_tools + https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats + 1.0 + perl-getopt-long + 2.54 + (0/1) + (0/1) + (0/1) + (0/1) + False combine_metaphlan_humann - 0.3.0 - python - To update + + combine_metaphlan_humann + Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann + combine_metaphlan_and_humann + Combine Metaphlan and HUMAnN + This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks - Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances - "This tool combine MetaPhlAn outputs and HUMANnN outputs." - Galaxy tool wrapper To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 + https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann + 0.3.0 + python + + (0/1) + (0/1) + (1/1) + (0/1) + False compare_humann2_output - 0.2.0 - - - To update + 332.0 + 10.0 + compare_humann2_output + Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs + compare_humann2_outputs + Compare HUMAnN2 outputs + This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families - Compare outputs of HUMAnN2 for several samples and extract similar and specific information - "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples." - Galaxy tool wrapper To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output + https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output + 0.2.0 + + + (0/1) + (0/1) + (0/1) + (0/1) + False - flye - 2.9.1 - 2.9.3 - flye - To update + compleasm + compleasm + Compleasm: a faster and more accurate reimplementation of BUSCO + compleasm + compleasm + compleasm + "Compleasm: a faster and more accurate reimplementation of BUSCO" + Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly + Sequence assembly, Genomics, Transcriptomics, Sequence analysis + Up-to-date + https://github.com/huangnengCSU/compleasm + Sequence Analysis + compleasm + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm + 0.2.6 + compleasm + 0.2.6 + (0/1) + (0/1) + (1/1) + (1/1) + False + + - Assembly of long and error-prone reads. + concoct + 250.0 + 29.0 + concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering + CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. + concoct + concoct - To update - https://github.com/fenderglass/Flye/ - Assembly - flye - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/flye + CONCOCT + A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. + Sequence clustering, Read binning + Metagenomics + Up-to-date + https://github.com/BinPro/CONCOCT + Metagenomics + concoct + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct + https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct + 1.1.0 + concoct + 1.1.0 + (0/5) + (0/5) + (5/5) + (5/5) + False - format_metaphlan2_output - 0.2.0 + coverm - To update - format_metaphlan2_output - Format metaphlan2 output - Formatting - Taxonomy, Metagenomics - Format MetaPhlAn2 output to extract abundance at different taxonomic levels - "This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)." - Galaxy tool wrapper - To update + coverm_contig, coverm_genome + CoverM genome and contig wrappers + coverm + coverm - Metagenomics - format_metaphlan2_output - bebatut - https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ + CoverM + Read coverage calculator for metagenomics + Local alignment + Bioinformatics + Up-to-date + https://github.com/wwood/CoverM + Sequence Analysis + coverm + iuc + https://github.com/galaxyproject/tools-iuc/tools/coverm + https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm + 0.7.0 + coverm + 0.7.0 + (0/2) + (0/2) + (2/2) + (2/2) + False - glimmer_hmm - + cryptogenotyper + 8518.0 + 16.0 + CryptoGenotyper + CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. - To update - GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) - To update - https://ccb.jhu.edu/software/glimmerhmm/ + Up-to-date + https://github.com/phac-nml/CryptoGenotyper Sequence Analysis - glimmer_hmm - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm + cryptogenotyper + nml + https://github.com/phac-nml/CryptoGenotyper + https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper + 1.0 + cryptogenotyper + 1.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - graphmap - 0.5.2 - 0.6.3 - graphmap - To update + cutadapt + 232004.0 + 5090.0 + cutadapt + Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). + cutadapt + cutadapt + Cutadapt + Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. + Sequence trimming, Primer removal, Read pre-processing + Genomics, Probes and primers, Sequencing + Up-to-date + https://cutadapt.readthedocs.org/en/stable/ + Fasta Manipulation, Fastq Manipulation, Sequence Analysis + cutadapt + lparsons + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt + 4.8 + cutadapt + 4.8 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + dada2 - Mapper for long, error-prone reads. + dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts + DADA2 wrappers + dada2 + dada2 + dada2 + This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. + Variant calling, DNA barcoding + Sequencing, Genetic variation, Microbial ecology, Metagenomics To update - https://github.com/isovic/graphmap/ - Assembly - graphmap - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/graphmap + https://benjjneb.github.io/dada2/index.html + Metagenomics + dada2 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 + + bioconductor-dada2 + 1.30.0 + (10/10) + (10/10) + (10/10) + (10/10) + False - iprscan5 + das_tool + 550.0 + 17.0 + Fasta_to_Contig2Bin, das_tool + DAS Tool for genome resolved metagenomics + dastool + dastool + dastool + DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. + Read binning + Metagenomics + Up-to-date + https://github.com/cmks/DAS_Tool + Metagenomics + das_tool + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool + https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool + 1.1.7 + das_tool + 1.1.7 + (0/2) + (0/2) + (2/2) + (2/2) + False + + + deseq2 + 95752.0 + 4990.0 + deseq2 + Differential gene expression analysis based on the negative binomial distribution + DESeq2 + DESeq2 + DESeq2 + R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + Differential gene expression analysis, RNA-Seq analysis + RNA-Seq To update + https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + Transcriptomics, RNA, Statistics + deseq2 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 + 2.11.40.8 + bioconductor-deseq2 + 1.42.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + diamond + 49711.0 + 963.0 + bg_diamond, bg_diamond_makedb, bg_diamond_view + DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. + diamond + diamond - - - Interproscan queries the interpro database and provides annotations. - + Diamond + Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. + Sequence alignment analysis + Sequence analysis, Proteins To update - http://www.ebi.ac.uk/Tools/pfa/iprscan5/ + https://github.com/bbuchfink/diamond Sequence Analysis - iprscan5 + diamond bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond + https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond + 2.0.15 + diamond + 2.1.9 + (3/3) + (3/3) + (3/3) + (3/3) + False - itsx - 1.1.3 - 1.1.3 - itsx - Up-to-date - ITSx - ITSx - Sequence feature detection - Functional, regulatory and non-coding RNA, Microbiology - ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. - TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. - Up-to-date - https://microbiology.se/software/itsx/ - Metagenomics - itsx - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/itsx - - + disco + 369.0 + 42.0 + disco + DISCO is a overlap-layout-consensus (OLC) metagenome assembler + disco + disco - lighter - 1.0 - 1.1.2 - lighter + DISCO + DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. + Protein sequence analysis + Structure determination To update + http://disco.omicsbio.org/ + Metagenomics, Assembly + disco + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco + disco + 1.2 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + dram - Lighter is a kmer-based error correction method for whole genome sequencing data + dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer + DRAM for distilling microbial metabolism to automate the curation of microbiome function + dram + dram + DRAM + Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes + Gene functional annotation + Metagenomics, Biological databases, Molecular genetics To update - - Sequence Analysis, Fasta Manipulation - lighter - bgruening - https://github.com/mourisl/Lighter + https://github.com/WrightonLabCSU/DRAM + Metagenomics + dram + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram + 1.3.5 + dram + 1.5.0 + (0/5) + (0/5) + (5/5) + (0/5) + False - mafft - 7.508 - 7.520 - mafft - To update - MAFFT - MAFFT - Multiple sequence alignment - Sequence analysis - Multiple alignment program for amino acid or nucleotide sequences - MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. - To update + drep - RNA - mafft - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/mafft + + drep_compare, drep_dereplicate + dRep compares and dereplicates genome sets + drep + drep + + dRep + Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. + Genome comparison + Metagenomics, Genomics, Sequence analysis + Up-to-date + https://github.com/MrOlm/drep + Metagenomics + drep + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep + https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep + 3.5.0 + drep + 3.5.0 + (0/2) + (0/2) + (2/2) + (2/2) + False - mcl - 14.137 - 22.282 - mcl - To update + ectyper + 9907.0 + 53.0 + ectyper + EC-Typer - in silico serotyping of Escherichia coli species + - Markov Cluster Algorithm - To update - http://micans.org/mcl/ - Sequence Analysis, Metagenomics - mcl - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/mcl - - - minipolish - 0.1.3 - 0.1.3 - minipolish - Up-to-date - minipolish - minipolish - Localised reassembly, Read depth analysis - Sequence assembly, Sequencing - Polishing miniasm assemblies - A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Up-to-date - https://github.com/rrwick/Minipolish + https://github.com/phac-nml/ecoli_serotyping Sequence Analysis - minipolish - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/minipolish - - - - nextdenovo - 2.5.0 - 2.5.2 - nextdenovo - To update - nextdenovo - NextDenovo - De-novo assembly, Genome assembly - Sequencing, Sequence assembly - String graph-based de novo assembler for long reads - NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. - To update - https://github.com/Nextomics/NextDenovo - Assembly - nextdenovo - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo + ectyper + nml + https://github.com/phac-nml/ecoli_serotyping + https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper + 1.0.0 + ectyper + 1.0.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - nucleosome_prediction - 3.0 - 3.0 - nucleosome_prediction - Up-to-date - - - + effectiveT3 - Prediction of Nucleosomes Positions on the Genome - Up-to-date - https://genie.weizmann.ac.il/software/nucleo_exe.html - Sequence Analysis - nucleosome_prediction - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction - - + effectiveT3 + Find bacterial type III effectors in protein sequences + effectivet3 + effectivet3 - pfamscan - 1.6 - 1.6 - pfam_scan - Up-to-date - pfamscan - PfamScan - Protein sequence analysis + EffectiveT3 + Prediction of putative Type-III secreted proteins. + Sequence classification Sequence analysis - Search a FASTA sequence against a library of Pfam HMM. - This tool is used to search a FASTA sequence against a library of Pfam HMM. - Up-to-date - http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ + To update + http://effectors.org Sequence Analysis - pfamscan - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan + effectivet3 + peterjc + https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 + https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 + 0.0.21 + effectiveT3 + 1.0.1 + (0/1) + (0/1) + (0/1) + (0/1) + False - racon - 1.5.0 - 1.5.0 - racon - Up-to-date - Racon - Racon - Genome assembly, Mapping assembly, Sequence trimming - Whole genome sequencing, Sequence assembly, Plant biology - Consensus module for raw de novo DNA assembly of long uncorrected reads. - The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads - Up-to-date - https://github.com/isovic/racon - Sequence Analysis - racon - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/racon - - + eggnog_mapper + 30565.0 + 510.0 + eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search + eggnog-mapper fast functional annotation of novel sequences + eggnog-mapper-v2 + eggnog-mapper-v2 - infernal - 1.1.4 - 1.1.4 - infernal - Up-to-date - infernal - Infernal - Nucleic acid feature detection - Sequence sites, features and motifs - Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. - Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. - Up-to-date - http://infernal.janelia.org/ - RNA - infernal - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/infernal + eggNOG-mapper v2 + EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. + Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval + Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis + To update + + Proteomics + eggnog_mapper + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper + 2.1.8 + eggnog-mapper + 2.1.12 + (3/3) + (3/3) + (3/3) + (3/3) + False - rRNA - 0.1 + emboss_5 + 89530.0 + 1816.0 + EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 + Galaxy wrappers for EMBOSS version 5.0.0 tools + emboss + emboss - hmmsearch3.0 + EMBOSS + Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. + Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment + Molecular biology, Sequence analysis, Biology To update + http://emboss.open-bio.org/ + Sequence Analysis, Fasta Manipulation + emboss_5 + devteam + https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 + 5.0.0 + emboss + 6.6.0 + (107/107) + (107/107) + (107/107) + (107/107) + False + + + ete + 1255.0 + 67.0 + ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator + Analyse phylogenetic trees using the ETE Toolkit + ete + ete - - - Identification of ribosomal RNA genes in metagenomic fragments. - + ete + The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org + Phylogenetic analysis, Phylogenetic tree editing + Phylogenetics To update - http://weizhong-lab.ucsd.edu/meta_rna/ - RNA - rrna - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/rRNA + http://etetoolkit.org/ + Phylogenetics + ete + earlhaminst + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete + 3.1.2 + ete3 + 3.1.1 + (0/7) + (0/7) + (7/7) + (7/7) + False - rbpbench - 0.8.1 - 0.8.1 - rbpbench - Up-to-date - rbpbench - RBPBench + export2graphlan + 5265.0 + 200.0 + export2graphlan + export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn + export2graphlan + export2graphlan - RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis - Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs - Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs - Up-to-date - https://github.com/michauhl/RBPBench - Sequence Analysis, RNA, CLIP-seq - rbpbench - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench + export2graphlan + export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. + Conversion + Taxonomy, Metabolomics, Biomarkers + To update + https://bitbucket.org/CibioCM/export2graphlan/overview + Metagenomics + export2graphlan + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan + 0.20 + export2graphlan + 0.22 + (1/1) + (1/1) + (1/1) + (1/1) + False - reago - 1.1 - 1.1 - reago - Up-to-date + ez_histograms + ez_histograms + ggplot2 histograms and density plots - Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. - Up-to-date - https://github.com/chengyuan/reago-1.1 - Metagenomics, RNA - reago - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago + + + + + To update + https://github.com/tidyverse/ggplot2 + Visualization, Statistics + ez_histograms + artbio + https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms + https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms + 3.4.4 + r-ggplot2 + 2.2.1 + (0/1) + (0/1) + (0/1) + (0/1) + False - sortmerna - 4.3.6 - 4.3.6 - sortmerna - Up-to-date - sortmerna - SortMeRNA - Sequence similarity search, Sequence comparison, Sequence alignment analysis - Metatranscriptomics, Metagenomics - SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. - Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. + fargene + 459.0 + 52.0 + fargene + fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + fargene + fargene + + fARGene + fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. + Antimicrobial resistance prediction + Metagenomics, Microbiology, Public health and epidemiology Up-to-date - http://bioinfo.lifl.fr/RNA/sortmerna/ - RNA - sortmerna - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna + https://github.com/fannyhb/fargene + Sequence Analysis + fargene + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene + 0.1 + fargene + 0.1 + (1/1) + (0/1) + (1/1) + (0/1) + False - salmon - 1.10.1 - 1.10.2 - salmon + fastani + 3498.0 + 250.0 + fastani + Fast alignment-free computation of whole-genome Average Nucleotide Identity + fastani + fastani + + FastANI + FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. + Genome alignment, Sequence similarity search + Microbiology, Genetic variation To update + https://github.com/ParBLiSS/FastANI + Sequence Analysis + fastani + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani + 1.3 + fastani + 1.34 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + fastk + + + fastk_fastk + FastK: A K-mer counter (for HQ assembly data sets) - Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. - To update - https://github.com/COMBINE-lab/salmon - Sequence Analysis, RNA, Transcriptomics - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/salmon - - - trim_galore - 0.6.7 - 0.6.10 - trim-galore - To update - trim_galore - Trim Galore - Sequence trimming - Sequence analysis - Trim Galore adaptive quality and adapter trimmer - A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. To update - http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ - Sequence Analysis, Fastq Manipulation - trim_galore - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore + https://github.com/thegenemyers/FASTK + Assembly + fastk + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk + 1.0.0 + fastk + 1.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - wtdbg - 2.5 - 2.5 - wtdbg - Up-to-date - wtdbg2 - wtdbg2 - Genome assembly, De-novo assembly - Sequence assembly, Sequencing - WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. + fastp + 1055760.0 + 2803.0 + fastp + Fast all-in-one preprocessing for FASTQ files + fastp + fastp + + fastp + A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + Sequencing quality control, Sequence contamination filtering + Sequence analysis, Probes and primers Up-to-date - https://github.com/ruanjue/wtdbg2 - Assembly - wtdbg - bgruening - https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg + https://github.com/OpenGene/fastp + Sequence Analysis + fastp + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp + 0.23.4 + fastp + 0.23.4 + (1/1) + (1/1) + (1/1) + (1/1) + False - clinod - 0.1.0 - 1.3 - clinod - To update + fastqe + 4333.0 + 1266.0 + fastqe + FASTQE + fastqe + fastqe + FASTQE + Compute quality stats for FASTQ files and print those stats as emoji... for some reason. + Sequencing quality control + Sequence analysis, Sequencing + To update + https://fastqe.com/ + Sequence Analysis + fastqe + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe + 0.3.1+galaxy0 + fastqe + 0.3.1 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + fasttree + 55434.0 + 379.0 + fasttree + FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL + fasttree + fasttree + FastTree + Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. + Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) + Phylogenetics, Sequence analysis + To update + http://www.microbesonline.org/fasttree/ + Phylogenetics + fasttree + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree + 2.1.10 + fasttree + 2.1.11 + (1/1) + (1/1) + (1/1) + (1/1) + False + + - NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins + featurecounts + 696399.0 + 4679.0 + featurecounts + featureCounts counts the number of reads aligned to defined masked regions in a reference genome + featurecounts + featurecounts + FeatureCounts + featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. + Read summarisation, RNA-Seq quantification + RNA-Seq To update - http://www.compbio.dundee.ac.uk/www-nod/ - Sequence Analysis - clinod - peterjc - https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod + http://bioinf.wehi.edu.au/featureCounts + RNA, Transcriptomics, Sequence Analysis + featurecounts + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts + https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts + 2.0.3 + subread + 2.0.6 + (1/1) + (1/1) + (1/1) + (1/1) + False - effectiveT3 - 0.0.20 - 1.0.1 - effectiveT3 - To update + filter_spades_repeats + filter_spades_repeat + Remove short and repeat contigs/scaffolds - Find bacterial type III effectors in protein sequences - To update - http://effectors.org - Sequence Analysis - effectivet3 - peterjc - https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 - - - abricate - 1.0.1 - 1.0.1 - abricate - Up-to-date - ABRicate - ABRicate - Antimicrobial resistance prediction - Genomics, Microbiology - Mass screening of contigs for antiobiotic resistance genes - Mass screening of contigs for antimicrobial resistance or virulence genes. - Up-to-date - https://github.com/tseemann/abricate - Sequence Analysis - abricate - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ - - - abritamr - 1.0.14 - 1.0.14 - abritamr - Up-to-date + To update + https://github.com/phac-nml/galaxy_tools/ + Assembly + filter_spades_repeats + nml + https://github.com/phac-nml/galaxy_tools/ + https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats + 1.0.1 + perl-bioperl + 1.7.8 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + filtlong + 30483.0 + 617.0 + filtlong + Filtlong - Filtering long reads by quality + filtlong + filtlong - A pipeline for running AMRfinderPlus and collating results into functional classes + Filtlong + Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + Filtering, Sequencing quality control Up-to-date - https://zenodo.org/record/7370628 - Sequence Analysis - abritamr + https://github.com/rrwick/Filtlong + Fastq Manipulation, Sequence Analysis + filtlong iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr + https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong + https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong + 0.2.1 + filtlong + 0.2.1 + (1/1) + (1/1) + (1/1) + (1/1) + False - abyss - 2.3.6 - 2.3.7 - abyss + flashlfq + 645.0 + 17.0 + flashlfq + FlashLFQ mass-spectrometry proteomics label-free quantification + flashlfq + flashlfq + + FlashLFQ + FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. + Label-free quantification + Proteomics experiment, Proteomics To update - abyss - ABySS - Genome assembly, De-novo assembly, Scaffolding - Sequence assembly - Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - De novo genome sequence assembler using short reads. + https://github.com/smith-chem-wisc/FlashLFQ + Proteomics + flashlfq + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq + 1.0.3.1 + flashlfq + 1.2.6 + (0/1) + (1/1) + (1/1) + (0/1) + False + + + + flye + 20904.0 + 1499.0 + flye + Assembly of long and error-prone reads. + Flye + Flye + + Flye + Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. + Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly + Sequence assembly, Metagenomics, Whole genome sequencing, Genomics To update - http://www.bcgsc.ca/platform/bioinfo/software/abyss + https://github.com/fenderglass/Flye/ Assembly - abyss - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss + flye + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/flye + https://github.com/bgruening/galaxytools/tree/master/tools/flye + 2.9.3 + flye + 2.9.4 + (1/1) + (1/1) + (1/1) + (1/1) + False - aldex2 - 1.26.0 - 1.34.0 - bioconductor-aldex2 - To update - aldex2 - ALDEx2 - Statistical inference - Gene expression, Statistics and probability - Performs analysis Of differential abundance taking sample variation into account - A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. + format_metaphlan2_output + 5588.0 + 166.0 + format_metaphlan2_output + Format MetaPhlAn2 output to extract abundance at different taxonomic levels + format_metaphlan2_output + format_metaphlan2_output + + Format metaphlan2 output + This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). + Formatting + Taxonomy, Metagenomics To update - https://github.com/ggloor/ALDEx_bioc + Metagenomics - aldex2 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 + format_metaphlan2_output + bebatut + https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ + https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output + 0.2.0 + + + (0/1) + (0/1) + (1/1) + (0/1) + False - amplican - 1.14.0 - 1.24.0 - bioconductor-amplican - To update - amplican - amplican - Alignment, Standardisation and normalisation - PCR experiment, Statistics and probability - AmpliCan is an analysis tool for genome editing. - It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. + fraggenescan + 1102.0 + 68.0 + fraggenescan + Tool for finding (fragmented) genes in short read + fraggenescan + fraggenescan + + FragGeneScan + Application for finding (fragmented) genes in short reads + Gene prediction + Genetics, Sequence analysis To update - https://github.com/valenlab/amplican + https://sourceforge.net/projects/fraggenescan/ Sequence Analysis - amplican + fraggenescan iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican - - + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan - amrfinderplus - 3.11.26 - 3.11.26 - ncbi-amrfinderplus - Up-to-date - amrfinderplus - AMRFinderPlus - Antimicrobial resistance prediction - Microbiology, Public health and epidemiology, Infectious disease - "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. - AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms - Up-to-date - https://github.com/ncbi/amr - Sequence Analysis - AMRFinderPlus - iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus + fraggenescan + 1.31 + (0/1) + (1/1) + (1/1) + (1/1) + False - ancombc - 1.4.0 - 2.4.0 - bioconductor-ancombc - To update - ancombc - ANCOMBC - DNA barcoding - Microbial ecology, Metagenomics - Performs analysis of compositions of microbiomes with bias correction. - Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. - To update - https://github.com/FrederickHuangLin/ANCOMBC - Metagenomics - ancombc - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc - - + freyja + + + freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants + lineage abundances estimation + freyja + freyja + - artic - 1.2.4 - artic - To update - artic - ARTIC - Sequence alignment - Genomics - The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building - A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore - To update - https://github.com/artic-network/fieldbioinformatics - Sequence Analysis - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic - - - bakta - 1.8.2 - 1.9.2 - bakta - To update - Bakta - Bakta - Genome annotation - Genomics, Data submission, annotation and curation, Sequence analysis - "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids To update - https://github.com/oschwengers/bakta - Sequence Analysis - bakta + https://github.com/andersen-lab/Freyja + Metagenomics, Sequence Analysis + freyja iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta + https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja + https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja + 1.4.4 + freyja + 1.5.0 + (2/4) + (0/4) + (4/4) + (0/4) + False - bandage - 2022.09 - 2022.09 - bandage_ng - Up-to-date - bandage - Bandage - Sequence assembly visualisation - Genomics, Sequence assembly - Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily - GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. + frogs + + + FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom + Suite for metabarcoding analysis + frogs + frogs + + FROGS + The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. + Taxonomic classification + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date - https://github.com/rrwick/Bandage - Visualization - bandage - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage + http://frogs.toulouse.inrae.fr/ + Metagenomics + frogs + frogs + https://github.com/geraldinepascal/FROGS-wrappers/ + https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + 4.1.0 + frogs + 4.1.0 + (0/28) + (0/28) + (0/28) + (28/28) + False - bayescan - 2.1 - 2.0.1 - bayescan - To update - bayescan - BayeScan - Statistical inference - Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism - Detecting natural selection from population-based genetic data - BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. - To update - http://cmpg.unibe.ch/software/BayeScan/index.html - Sequence Analysis - bayescan - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ - - + frogs - binning_refiner - 1.4.3 - 1.4.3 - binning_refiner - Up-to-date - binning_refiner - Binning_refiner - Read binning, Sequence clustering - Metagenomics - Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. - Improving genome bins through the combination of different binning programs + + FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom + Suite for metabarcoding analysis + frogs + frogs + + FROGS + The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. + Taxonomic classification + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date - https://github.com/songweizhi/Binning_refiner + http://frogs.toulouse.inrae.fr/ Metagenomics - binning_refiner - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ + frogs + frogs + https://github.com/geraldinepascal/FROGS-wrappers/ + https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + 4.1.0 + frogs + 4.1.0 + (0/28) + (0/28) + (0/28) + (28/28) + False - biom_format - 2.1.15 - 2.1.7 - biom-format - To update + frogs + FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom + Suite for metabarcoding analysis + frogs + frogs + FROGS + The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. + Taxonomic classification + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing + Up-to-date + http://frogs.toulouse.inrae.fr/ + Metagenomics + frogs + frogs + https://github.com/geraldinepascal/FROGS-wrappers/ + https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + 4.1.0 + frogs + 4.1.0 + (0/28) + (0/28) + (0/28) + (28/28) + False + + - The biom-format package provides a command line interface and Python API for working with BIOM files. + frogs - To update - https://github.com/biocore/biom-format - Metagenomics - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format + FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom + Suite for metabarcoding analysis + frogs + frogs + + FROGS + The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. + Taxonomic classification + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing + Up-to-date + http://frogs.toulouse.inrae.fr/ + Metagenomics + frogs + frogs + https://github.com/geraldinepascal/FROGS-wrappers/ + https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + 4.1.0 + frogs + 4.1.0 + (0/28) + (0/28) + (0/28) + (28/28) + False - bracken - 2.9 - 2.9 - bracken - Up-to-date - bracken - Bracken - Statistical calculation - Metagenomics, Microbial ecology - Bayesian Reestimation of Abundance with KrakEN - Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + frogs + + + FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom + Suite for metabarcoding analysis + frogs + frogs + + FROGS + The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. + Taxonomic classification + Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date - https://ccb.jhu.edu/software/bracken/ - Sequence Analysis, Metagenomics - bracken - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken + http://frogs.toulouse.inrae.fr/ + Metagenomics + frogs + frogs + https://github.com/geraldinepascal/FROGS-wrappers/ + https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs + 4.1.0 + frogs + 4.1.0 + (0/28) + (0/28) + (0/28) + (28/28) + False - busco - 5.5.0 - 5.6.1 - busco - To update - busco - BUSCO - Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly - Sequence assembly, Genomics, Transcriptomics, Sequence analysis - BUSCO assess genome and annotation completeness - Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + funannotate + + + funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort + Funannotate is a genome prediction, annotation, and comparison software package. + funannotate + funannotate + + funannotate + funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). + Genome annotation + Genomics To update - https://gitlab.com/ezlab/busco/-/releases - Sequence Analysis - busco + https://funannotate.readthedocs.io + Genome annotation + iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate + https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate + 1.8.15 + + + (3/5) + (5/5) + (5/5) + (5/5) + False - cat - 5.2.3 - 5.3 - cat - To update + getmlst + + + getmlst + Download MLST datasets by species from pubmlst.org + + - Contig Annotation Tool (CAT) To update - https://github.com/dutilh/CAT - Metagenomics - contig_annotation_tool - iuc - https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat - - - cdhit - 4.8.1 - 4.8.1 - cd-hit - Up-to-date - cd-hit - cd-hit - Sequence clustering - Sequencing - Cluster or compare biological sequence datasets - Cluster a nucleotide dataset into representative sequences. - Up-to-date - http://weizhongli-lab.org/cd-hit/ - Sequence Analysis, Fasta Manipulation - cd_hit - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit + Sequence Analysis + getmlst + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst + 0.1.4.1 + srst2 + 0.2.0 + (0/1) + (0/1) + (0/1) + (0/1) + False - cemitool - 1.18.1 - 1.26.0 - bioconductor-cemitool - To update - cemitool - CEMiTool - Enrichment analysis, Pathway or network analysis - Gene expression, Transcriptomics, Microarray experiment - Gene co-expression network analysis tool - It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + ggplot2 + + + ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin + ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. + ggplot2 + ggplot2 + + ggplot2 + Plotting system for R, based on the grammar of graphics. + Visualisation + Data visualisation To update - https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html - Transcriptomics, RNA, Statistics - cemitool + https://github.com/tidyverse/ggplot2 + Visualization + iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool + https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 + 3.4.0 + r-base + + (5/5) + (5/5) + (5/5) + (5/5) + False - checkm - 1.2.0 - 1.2.2 - checkm-genome - To update - checkm - CheckM - Operation - Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics - Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes - CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + gi2taxonomy + 660.0 + 27.0 + Fetch Taxonomic Ranks + Fetch taxonomic representation + gi2taxonomy + gi2taxonomy + + gi2taxonomy + The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). + Database search, ID mapping + Taxonomy To update - https://github.com/Ecogenomics/CheckM + https://bitbucket.org/natefoo/taxonomy Metagenomics - checkm - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm + gi2taxonomy + devteam + https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy + 1.1.1 + taxonomy + 0.10.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - clustalw - 2.1 - 2.1 - clustalw - Up-to-date - \n clustal2\n + glimmer + glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based + Glimmer makes gene predictions. + gemini + gemini - ClustalW multiple sequence alignment program for DNA or proteins + GEMINI + GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. + Sequence analysis, Genetic variation analysis + Sequence analysis + To update + https://ccb.jhu.edu/software/glimmer/ + Sequence Analysis - Up-to-date - http://www.clustal.org/clustal2/ - Phylogenetics, Sequence Analysis - clustalw - devteam - https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw + bgruening + https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer + https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer + + glimmer + 3.02 + (0/8) + (0/8) + (4/8) + (0/8) + False - codeml - 4.9 - 4.10.7 - paml - To update + glimmer_hmm + + + + GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) + + - Detects positive selection To update - http://abacus.gene.ucl.ac.uk/software/paml.html - Phylogenetics - codeml - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml + https://ccb.jhu.edu/software/glimmerhmm/ + Sequence Analysis + glimmer_hmm + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm + https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm + + + + (0/1) + (0/1) + (0/1) + (0/1) + False - cojac - 0.9.1 - 0.9.1 - cojac - Up-to-date - cojac - COJAC + goenrichment + 5206.0 + 321.0 + goenrichment, goslimmer + Performs GO Enrichment analysis. + goenrichment + goenrichment - Genetic variation - co-occurrence of mutations on amplicons - CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. + GOEnrichment + GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. + Gene-set enrichment analysis + Transcriptomics Up-to-date - https://github.com/cbg-ethz/cojac - Metagenomics, Sequence Analysis - cojac + https://github.com/DanFaria/GOEnrichment + Genome annotation + iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac + https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment + https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment + 2.0.1 + goenrichment + 2.0.1 + (2/2) + (2/2) + (2/2) + (2/2) + False - concoct - 1.1.0 - 1.1.0 - concoct - Up-to-date - concoct - CONCOCT - Sequence clustering, Read binning - Metagenomics - CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. - A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. - Up-to-date - https://github.com/BinPro/CONCOCT - Metagenomics - concoct + goseq + 19167.0 + 1210.0 + goseq + goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data + goseq + goseq + + GOseq + Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + Gene functional annotation + RNA-Seq + To update + https://bioconductor.org/packages/release/bioc/html/goseq.html + Statistics, RNA, Micro-array Analysis + goseq iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct + https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq + 1.50.0 + bioconductor-goseq + 1.54.0 + (1/1) + (1/1) + (1/1) + (1/1) + False - coverm - 0.6.1 - 0.7.0 - coverm - To update - coverm - CoverM - Local alignment - Bioinformatics - CoverM genome and contig wrappers - Read coverage calculator for metagenomics + graphlan + 5002.0 + 247.0 + graphlan, graphlan_annotate + GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees + graphlan + graphlan + + GraPhlAn + GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. + Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification + Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update - https://github.com/wwood/CoverM - Sequence Analysis - coverm + https://github.com/biobakery/graphlan + Metagenomics, Graphics, Phylogenetics + graphlan iuc - https://github.com/galaxyproject/tools-iuc/tools/coverm + https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan + + graphlan + 1.1.3 + (2/2) + (2/2) + (2/2) + (2/2) + False - cutadapt - 4.6 - 4.6 - cutadapt - Up-to-date - cutadapt - Cutadapt - Sequence trimming - Genomics, Probes and primers, Sequencing - Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). - Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. - Up-to-date - https://cutadapt.readthedocs.org/en/stable/ - Fasta Manipulation, Fastq Manipulation, Sequence Analysis - cutadapt - lparsons - https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt + graphmap + + + graphmap_align, graphmap_overlap + Mapper for long, error-prone reads. + graphmap + graphmap + + graphmap + Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 + Sequence trimming, EST assembly, Read mapping + Gene transcripts, RNA-Seq, RNA splicing + To update + https://github.com/isovic/graphmap/ + Assembly + graphmap + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/graphmap + https://github.com/bgruening/galaxytools/tree/master/tools/graphmap + 0.5.2 + graphmap + 0.6.3 + (0/2) + (0/2) + (2/2) + (0/2) + False - dada2 + gtdbtk - 1.30.0 - bioconductor-dada2 - To update - dada2 - dada2 - Variant calling, DNA barcoding - Sequencing, Genetic variation, Microbial ecology, Metagenomics - DADA2 wrappers - This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. + + gtdbtk_classify_wf + GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. + GTDB-Tk + GTDB-Tk + + GTDB-Tk + a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). + Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval + Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update - https://benjjneb.github.io/dada2/index.html + https://github.com/Ecogenomics/GTDBTk Metagenomics - dada2 + gtdbtk iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk + https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk + 2.3.2 + gtdbtk + 2.4.0 + (0/1) + (1/1) + (1/1) + (0/1) + False - das_tool - 1.1.6 - 1.1.7 - das_tool - To update - dastool - dastool - Read binning - Metagenomics - DAS Tool for genome resolved metagenomics - DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. + gubbins + 3340.0 + 145.0 + gubbins + Gubbins - bacterial recombination detection + gubbins + gubbins + + Gubbins + Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. + Genotyping, Phylogenetic inference, Ancestral reconstruction + Phylogeny, Genotype and phenotype, Whole genome sequencing To update - https://github.com/cmks/DAS_Tool - Metagenomics - das_tool + + Sequence Analysis + gubbins iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool + https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins + https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins + 3.2.1 + gubbins + 3.3.5 + (1/1) + (1/1) + (1/1) + (0/1) + False - diamond - 2.0.15 - 2.1.8 - diamond - To update - diamond - Diamond - Sequence alignment analysis - Sequence analysis, Proteins - DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. - Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. - To update - https://github.com/bbuchfink/diamond - Sequence Analysis - diamond - bgruening - https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond - - + hamronization - disco - 1.2 - disco - To update - disco - DISCO - Protein sequence analysis - Structure determination - DISCO is a overlap-layout-consensus (OLC) metagenome assembler - DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. - To update - http://disco.omicsbio.org/ - Metagenomics, Assembly - disco + hamronize_summarize, hamronize_tool + Convert AMR gene detection tool output to hAMRonization specification format. + hamronization + hamronization + + hAMRonization + Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure + Data handling, Antimicrobial resistance prediction, Parsing + Public health and epidemiology, Microbiology, Bioinformatics + Up-to-date + https://github.com/pha4ge/hAMRonization + Sequence Analysis + hamronization iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization + 1.1.4 + hamronization + 1.1.4 + (0/2) + (0/2) + (2/2) + (2/2) + False - dram - 1.3.5 - 1.4.6 - dram - To update - - + hansel - DRAM for distilling microbial metabolism to automate the curation of microbiome function + bio_hansel + Heidelberg and Enteritidis SNP Elucidation + Biohansel + Biohansel - To update - https://github.com/WrightonLabCSU/DRAM - Metagenomics - dram + BioHansel + BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. + Genotyping, SNP detection, Genome assembly + Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science + Up-to-date + https://github.com/phac-nml/bio_hansel + Sequence Analysis + bio_hansel iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel + 2.6.1 + bio_hansel + 2.6.1 + (1/1) + (0/1) + (1/1) + (0/1) + False - drep - 3.4.5 - 3.4.5 - drep - Up-to-date - drep - dRep - Genome comparison - Metagenomics, Genomics, Sequence analysis - dRep compares and dereplicates genome sets - Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. - Up-to-date - https://github.com/MrOlm/drep + hifiasm_meta + 137.0 + 12.0 + hifiasm_meta + A hifiasm fork for metagenome assembly using Hifi reads. + hifiasm-meta + hifiasm-meta + + Hifiasm-meta + Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. + Sequence assembly + Sequence assembly, Metagenomics + To update + https://github.com/xfengnefx/hifiasm-meta Metagenomics - drep - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep + hifiasm_meta + galaxy-australia + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta + 0.3.1 + hifiasm_meta + hamtv0.3.1 + (0/1) + (1/1) + (1/1) + (0/1) + False - export2graphlan - 0.20 - 0.22 - export2graphlan - To update + hivtrace + hivtrace + An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. - export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn - To update - https://bitbucket.org/CibioCM/export2graphlan/overview - Metagenomics - export2graphlan - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ - - - fargene - 0.1 - 0.1 - fargene - Up-to-date + To update - fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) + Sequence Analysis + hivtrace + nml + https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace + https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace + 1.0.1 + hivtrace + 1.5.0 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + hmmer3 + 21049.0 + 111.0 + hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer + HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). + hmmer3 + hmmer3 + HMMER3 + This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. + Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search + Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date - https://github.com/fannyhb/fargene + http://hmmer.org/ Sequence Analysis - fargene + iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 + 3.4 + hmmer + 3.4 + (0/12) + (12/12) + (12/12) + (12/12) + False - fastp + humann + 5856.0 + 247.0 + humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways + HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution + humann + humann - 0.23.4 - fastp - To update - \n fastp\n + humann + HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” + Species frequency estimation, Taxonomic classification, Phylogenetic analysis + Metagenomics, Phylogenomics + Up-to-date + http://huttenhower.sph.harvard.edu/humann + Metagenomics + humann + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann + https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann + 3.8 + humann + 3.8 + (6/13) + (12/13) + (13/13) + (13/13) + False + + + hyphy - Fast all-in-one preprocessing for FASTQ files + hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary + Hypothesis Testing using Phylogenies + HyPhy + HyPhy + HyPhy + Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. + Statistical calculation + Phylogeny, Small molecules, Molecular interactions, pathways and networks To update - https://github.com/OpenGene/fastp - Sequence Analysis - fastp + http://www.hyphy.org + Phylogenetics + iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy + 2.5.47 + hyphy + 2.5.62 + (17/17) + (2/17) + (17/17) + (2/17) + False - fastqe - 0.3.1+galaxy0 - 0.3.1 - fastqe - To update + hypo + 354.0 + 39.0 + hypo + Super Fast & Accurate Polisher for Long Read Genome Assemblies + HyPo + HyPo + HyPo + HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. + Optimisation and refinement, Genome assembly + Sequence assembly, Genomics + Up-to-date + https://github.com/kensung-lab/hypo + Assembly + hypo + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo + https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo + 1.0.3 + hypo + 1.0.3 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + icescreen - FASTQE + icescreen + ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. + icescreen + icescreen + ICEscreen + A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. + Database search, Protein feature detection + Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe - Sequence Analysis - fastqe + https://icescreen.migale.inrae.fr/ + Genome annotation + icescreen iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe + https://forgemia.inra.fr/ices_imes_analysis/icescreen + https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen + 1.3.1 + icescreen + 1.3.2 + (0/1) + (0/1) + (0/1) + (0/1) + False - fasttree - 2.1.10 - 2.1.11 - fasttree + idba_ud + 721.0 + 43.0 + idba_hybrid, idba_tran, idba_ud + Wrappers for the idba assembler variants. + idba + idba + + IDBA + A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. + Sequence assembly + Sequence assembly To update - fasttree - FastTree - Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) - Phylogenetics, Sequence analysis - FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL - Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. - To update - http://www.microbesonline.org/fasttree/ - Phylogenetics - fasttree + https://i.cs.hku.hk/~alse/hkubrg/projects/index.html + Assembly + idba iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree + https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud + https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud + + idba + 1.1.3 + (3/3) + (0/3) + (3/3) + (3/3) + False - filtlong - 0.2.1 - 0.2.1 - filtlong - Up-to-date - \n filtlong\n + infernal + 100230.0 + 67.0 + infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. + infernal + infernal + + Infernal + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. + Nucleic acid feature detection + Sequence sites, features and motifs, Structural genomics + To update + http://infernal.janelia.org/ + RNA + infernal + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/infernal + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal + 1.1.4 + infernal + 1.1.5 + (0/6) + (6/6) + (6/6) + (0/6) + False + + + instrain - Filtlong - Filtering long reads by quality + instrain_compare, instrain_profile + InStrain is a tool for analysis of co-occurring genome populations from metagenomes + instrain + instrain - Up-to-date - https://github.com/rrwick/Filtlong - Fastq Manipulation, Sequence Analysis - filtlong + InStrain + InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification + SNP detection, Genome comparison + Mapping, Metagenomics + To update + https://instrain.readthedocs.io/en/latest/# + Metagenomics + instrain iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong + https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain + https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain + 1.5.3 + instrain + 1.9.0 + (0/2) + (0/2) + (2/2) + (0/2) + False - fraggenescan + integron_finder + 52965.0 + 58.0 + integron_finder + "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" + integron_finder + integron_finder - 1.31 - fraggenescan - To update - fraggenescan - FragGeneScan - Gene prediction - Genetics, Sequence analysis - Tool for finding (fragmented) genes in short read - Application for finding (fragmented) genes in short reads - To update - https://sourceforge.net/projects/fraggenescan/ + Integron Finder + A tool to detect Integron in DNA sequences. + Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation + Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis + Up-to-date + https://github.com/gem-pasteur/Integron_Finder Sequence Analysis - fraggenescan + integronfinder iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ + https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder + https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder + 2.0.3 + integron_finder + 2.0.3 + (0/1) + (1/1) + (1/1) + (1/1) + False - freyja - 1.4.4 - 1.4.8 - freyja - To update - freyja - - - - lineage abundances estimation + interproscan + 5294.0 + 554.0 + interproscan + Interproscan queries the interpro database and provides annotations. + interproscan_ebi + interproscan_ebi + InterProScan (EBI) + Scan sequences against the InterPro protein signature databases. + Sequence motif recognition, Protein feature detection + Gene and protein families, Sequence analysis To update - https://github.com/andersen-lab/Freyja - Metagenomics, Sequence Analysis - freyja - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja + http://www.ebi.ac.uk/Tools/pfa/iprscan5/ + Sequence Analysis + interproscan + bgruening + https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan + https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan + 5.59-91.0 + interproscan + 5.59_91.0 + (1/1) + (1/1) + (1/1) + (1/1) + False - funannotate - 1.8.15 + iprscan5 - To update - \n funannotate\n + + Interproscan queries the interpro database and provides annotations. - Funannotate is a genome prediction, annotation, and comparison software package. - To update - https://funannotate.readthedocs.io - Genome annotation - iuc - https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate - - - glimmer - 3.02 - glimmer - To update - gemini - GEMINI - Sequence analysis, Genetic variation analysis - Sequence analysis - Glimmer makes gene predictions. - GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. To update - https://ccb.jhu.edu/software/glimmer/ + http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis - + iprscan5 bgruening - https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer + https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 + https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 + + + + (0/1) + (0/1) + (0/1) + (0/1) + False - goenrichment - 2.0.1 - 2.0.1 - goenrichment - Up-to-date - goenrichment - GOEnrichment - Gene-set enrichment analysis - Transcriptomics - Performs GO Enrichment analysis. - GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. - Up-to-date - https://github.com/DanFaria/GOEnrichment - Genome annotation + iqtree + 21598.0 + 681.0 + iqtree + Efficient phylogenomic software by maximum likelihood + iqtree + iqtree + iqtree + A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time + Phylogenetic analysis, Sequence analysis + Phylogenetics + Up-to-date + http://www.iqtree.org/ + Phylogenetics + iqtree iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment + https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree + 2.3.4 + iqtree + 2.3.4 + (1/1) + (1/1) + (1/1) + (0/1) + False - goseq - 1.50.0 - 1.54.0 - bioconductor-goseq - To update - goseq - GOseq - Gene functional annotation - RNA-Seq - goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data - Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + isescan + 57581.0 + 50.0 + isescan + "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." + ISEScan + ISEScan + + ISEScan + Automated identification of insertion sequence elements in prokaryotic genomes. + Structural variation detection + Genomics, DNA structural variation, Sequence analysis, Genetic variation To update - https://bioconductor.org/packages/release/bioc/html/goseq.html - Statistics, RNA, Micro-array Analysis - goseq + https://github.com/xiezhq/ISEScan + Sequence Analysis + ISEScan iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq + https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan + https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan + 1.7.2.3 + isescan + 1.7.2.1 + (0/1) + (1/1) + (1/1) + (1/1) + False - graphlan + itsx + 868.0 + 38.0 + itsx + ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. + ITSx + ITSx + ITSx + TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. + Sequence feature detection + Functional, regulatory and non-coding RNA, Microbiology + Up-to-date + https://microbiology.se/software/itsx/ + Metagenomics + itsx + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/itsx + https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 - graphlan - To update - - - - - GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees - - To update - https://bitbucket.org/nsegata/graphlan/overview - Metagenomics, Graphics, Phylogenetics - graphlan - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ + itsx + 1.1.3 + (0/1) + (0/1) + (1/1) + (0/1) + False - gtdbtk - 2.2.2 - 2.3.2 - gtdbtk - To update + ivar + + + ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants + iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing - GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. - To update - https://github.com/Ecogenomics/GTDBTk - Metagenomics - gtdbtk - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk - - - gubbins - 3.2.1 - 3.3.1 - gubbins - To update - gubbins - Gubbins - Genotyping, Phylogenetic inference, Ancestral reconstruction - Phylogeny, Genotype and phenotype, Whole genome sequencing - Gubbins - bacterial recombination detection - Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. - To update + Up-to-date + https://github.com/andersen-lab/ivar Sequence Analysis - gubbins + ivar iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins + https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar + 1.4.2 + ivar + 1.4.2 + (5/5) + (5/5) + (5/5) + (5/5) + False - hamronization - 1.0.3 - 1.1.4 - hamronization - To update - - - - - Convert AMR gene detection tool output to hAMRonization specification format. + jbrowse + 18229.0 + 2346.0 + jbrowse_to_standalone, jbrowse + JBrowse Genome Browser integrated as a Galaxy Tool + jbrowse + jbrowse - To update - https://github.com/pha4ge/hAMRonization + JBrowse + Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. + Genome visualisation + Genomics + Up-to-date + https://jbrowse.org Sequence Analysis - hamronization + jbrowse iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization + https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse + https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse + 1.16.11 + jbrowse + 1.16.11 + (2/2) + (2/2) + (2/2) + (2/2) + False - hansel - 2.6.1 - 2.6.1 - bio_hansel - Up-to-date - Biohansel - BioHansel - Genotyping, SNP detection, Genome assembly - Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science - Heidelberg and Enteritidis SNP Elucidation - BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. - Up-to-date - https://github.com/phac-nml/bio_hansel - Sequence Analysis - bio_hansel + jellyfish + 1138.0 + 91.0 + jellyfish + Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA + Jellyfish + Jellyfish + + Jellyfish + A command-line algorithm for counting k-mers in DNA sequence. + k-mer counting + Sequence analysis, Genomics + To update + https://github.com/gmarcais/Jellyfish + Assembly + jellyfish iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel + https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish + https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish + + kmer-jellyfish + 2.3.1 + (0/1) + (1/1) + (1/1) + (1/1) + False - hifiasm_meta - 0.3.1 - hamtv0.3.1 - hifiasm_meta - To update + kat_filter + + + kat_@EXECUTABLE@ + Filtering kmers or reads from a database of kmers hashes + - A hifiasm fork for metagenome assembly using Hifi reads. - To update - https://github.com/xfengnefx/hifiasm-meta - Metagenomics - hifiasm_meta - galaxy-australia - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta - - - hmmer3 - 3.3.2 - 3.4 - hmmer - To update - hmmer3 - HMMER3 - Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search - Sequence analysis, Sequence sites, features and motifs, Gene and protein families - HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). - This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. To update - http://hmmer.org/ + Sequence Analysis + kat_filter + nml - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 + https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter + 2.3 + kat + 2.4.2 + (0/1) + (0/1) + (0/1) + (0/1) + False - humann - 3.8 - 3.8 - humann - Up-to-date - humann - humann - Species frequency estimation, Taxonomic classification, Phylogenetic analysis - Metagenomics, Phylogenomics - HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution - HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” + kc-align + + + kc-align + Kc-Align custom tool + kc-align + kc-align + + kc-align + A fast and accurate tool for performing codon-aware multiple sequence alignments + Multiple sequence alignment + Mapping Up-to-date - http://huttenhower.sph.harvard.edu/humann - Metagenomics - humann + https://github.com/davebx/kc-align + Sequence Analysis + kc_align iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align + 1.0.2 + kcalign + 1.0.2 + (1/1) + (0/1) + (1/1) + (0/1) + False - hyphy - 2.5.47 - 2.5.59 - hyphy - To update - HyPhy - HyPhy - Statistical calculation - Phylogeny, Small molecules, Molecular interactions, pathways and networks - Hypothesis Testing using Phylogenies - Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. - To update - http://www.hyphy.org - Phylogenetics + khmer + + + khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median + In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more + khmer + khmer + khmer + khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. + Standardisation and normalisation, De-novo assembly + Sequence assembly + Up-to-date + https://khmer.readthedocs.org/ + Assembly, Next Gen Mappers + khmer iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ + https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer + https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer + 3.0.0a3 + khmer + 3.0.0a3 + (8/8) + (8/8) + (8/8) + (0/8) + False - hypo - 1.0.3 - 1.0.3 - hypo - Up-to-date - HyPo - HyPo - Optimisation and refinement, Genome assembly - Sequence assembly, Genomics - Super Fast & Accurate Polisher for Long Read Genome Assemblies - HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. + kleborate + 319.0 + 38.0 + kleborate + Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) + kleborate + kleborate + + Kleborate + Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). + Multilocus sequence typing, Genome assembly, Virulence prediction + Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date - https://github.com/kensung-lab/hypo - Assembly - hypo + https://github.com/katholt/Kleborate/wiki + Metagenomics + kleborate iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo + https://github.com/katholt/Kleborate + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate + 2.3.2 + kleborate + 2.3.2 + (0/1) + (0/1) + (1/1) + (0/1) + False - icescreen - 1.3.1 - 1.3.1 - icescreen - Up-to-date - - - - - ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. + kofamscan + 594.0 + 33.0 + kofamscan + Gene function annotation tool based on KEGG Orthology and hidden Markov model + kofamscan + kofamscan + kofamscan + KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. + Sequence analysis, Gene functional annotation + Genomics Up-to-date - https://icescreen.migale.inrae.fr/ - Genome annotation - icescreen + https://github.com/takaram/kofam_scan + Sequence Analysis + kofamscan iuc - https://forgemia.inra.fr/ices_imes_analysis/icescreen + https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan + 1.3.0 + kofamscan + 1.3.0 + (0/1) + (0/1) + (1/1) + (1/1) + False - idba_ud + kraken + 13938.0 + 404.0 + kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken + Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. + kraken + kraken - 1.1.3 - idba - To update - idba - IDBA - Sequence assembly - Sequence assembly - Wrappers for the idba assembler variants. - A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. + Kraken + System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. + Taxonomic classification + Taxonomy, Metagenomics To update - https://i.cs.hku.hk/~alse/hkubrg/projects/index.html - Assembly - idba - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud + http://ccb.jhu.edu/software/kraken/ + Metagenomics + kraken + devteam + https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ + https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken + + kraken + 1.1.1 + (5/5) + (5/5) + (5/5) + (5/5) + False - instrain - 1.5.3 - 1.8.0 - instrain - To update - instrain - InStrain - SNP detection, Genome comparison - Mapping, Metagenomics - InStrain is a tool for analysis of co-occurring genome populations from metagenomes - InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification - To update - https://instrain.readthedocs.io/en/latest/# - Metagenomics - instrain - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain - - - - interproscan - 5.59-91.0 - 5.59_91.0 - interproscan - To update - interproscan_ebi - InterProScan (EBI) - Sequence motif recognition, Protein feature detection - Gene and protein families, Sequence analysis - Interproscan queries the interpro database and provides annotations. - Scan sequences against the InterPro protein signature databases. - To update - http://www.ebi.ac.uk/Tools/pfa/iprscan5/ - Sequence Analysis - interproscan - bgruening - https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan - - - - iqtree - 2.1.2 - 2.2.6 - iqtree - To update - - - - - Efficient phylogenomic software by maximum likelihood + kraken2 + 185308.0 + 2367.0 + kraken2 + Kraken2 for taxonomic designation. + kraken2 + kraken2 + kraken2 + Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. + Taxonomic classification + Taxonomy, Metagenomics To update - http://www.iqtree.org/ - Phylogenetics - iqtree + http://ccb.jhu.edu/software/kraken/ + Metagenomics + kraken2 iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ + https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ + https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 + 2.1.1 + kraken2 + 2.1.3 + (1/1) + (1/1) + (1/1) + (1/1) + False - ivar - 1.4.2 - 1.4.2 - ivar - Up-to-date - + kraken2tax + 14683.0 + 481.0 + Kraken2Tax + Convert Kraken output to Galaxy taxonomy data. - iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing - Up-to-date - https://github.com/andersen-lab/ivar - Sequence Analysis - ivar - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ - - - jbrowse - 1.16.11 - 1.16.11 - jbrowse - Up-to-date - jbrowse - JBrowse - Genome visualisation - Genomics - JBrowse Genome Browser integrated as a Galaxy Tool - Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. - Up-to-date - https://jbrowse.org - Sequence Analysis - jbrowse - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse - - - jellyfish - 2.3.0 - kmer-jellyfish - To update - Jellyfish - Jellyfish - k-mer counting - Sequence analysis, Genomics - Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA - A command-line algorithm for counting k-mers in DNA sequence. To update - https://github.com/gmarcais/Jellyfish - Assembly - jellyfish - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish - - - - kc-align - 1.0.2 - 1.0.2 - kcalign - Up-to-date - kc-align - kc-align - Multiple sequence alignment - Mapping - Kc-Align custom tool - A fast and accurate tool for performing codon-aware multiple sequence alignments - Up-to-date - https://github.com/davebx/kc-align - Sequence Analysis - kc_align - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align - - - - khmer - 3.0.0a3 - 3.0.0a3 - khmer - Up-to-date - khmer - khmer - Standardisation and normalisation, De-novo assembly - Sequence assembly - In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more - khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. - Up-to-date - https://khmer.readthedocs.org/ - Assembly, Next Gen Mappers - khmer - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer - - - - kleborate - 2.3.2 - 2.3.2 - kleborate - Up-to-date - kleborate - Kleborate - Multilocus sequence typing, Genome assembly, Virulence prediction - Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing - Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) - Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). - Up-to-date - https://github.com/katholt/Kleborate/wiki + https://bitbucket.org/natefoo/taxonomy Metagenomics - kleborate - iuc - https://github.com/katholt/Kleborate - - - - kofamscan - 1.3.0 - 1.3.0 - kofamscan - Up-to-date - - - - - Gene function annotation tool based on KEGG Orthology and hidden Markov model + kraken2tax + devteam + https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax + 1.2+galaxy0 + gawk - Up-to-date - https://github.com/takaram/kofam_scan - Sequence Analysis - kofamscan - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan + (1/1) + (1/1) + (1/1) + (0/1) + False kraken_biom - 1.2.0 - 1.2.0 - kraken-biom - Up-to-date + 1444.0 + 182.0 + kraken_biom + Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) + + - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom @@ -2576,2166 +3737,7185 @@ kraken_biom iuc https://github.com/smdabdoub/kraken-biom + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom + 1.2.0 + kraken-biom + 1.2.0 + (0/1) + (1/1) + (1/1) + (1/1) + False kraken_taxonomy_report - 0.0.3 - 1.70 - biopython - To update - - - - + 2527.0 + 354.0 + kraken_taxonomy_report Kraken taxonomy report + Kraken-Taxonomy-Report + Kraken-Taxonomy-Report + Kraken-Taxonomy-Report + view report of classification for multiple samples + Visualisation, Classification + Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report + https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report + 0.0.3 + biopython + 1.70 + (1/1) + (1/1) + (1/1) + (0/1) + False krakentools - 1.2 - 1.2 + + + krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa + KrakenTools is a suite of scripts to be used alongside the Kraken krakentools - Up-to-date krakentools + KrakenTools + KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics - KrakenTools is a suite of scripts to be used alongside the Kraken - KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools + https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools + 1.2 + krakentools + 1.2 + (1/6) + (6/6) + (6/6) + (6/6) + False krocus - 1.0.1 - 1.0.3 - krocus - To update - - + krocus Predict MLST directly from uncorrected long reads + krocus + krocus + krocus + Predict MLST directly from uncorrected long reads + Multilocus sequence typing, k-mer counting + Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus + https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus + 1.0.1 + krocus + 1.0.3 + (0/1) + (0/1) + (1/1) + (0/1) + False - legsta - 0.5.1 - 0.5.1 - legsta - Up-to-date + lca_wrapper + 137.0 + 2.0 + lca1 + Find lowest diagnostic rank + + + + To update + https://bitbucket.org/natefoo/taxonomy + Metagenomics + lca_wrapper + devteam + https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper + 1.0.1 + taxonomy + 0.10.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + legsta + 55.0 + 7.0 + legsta Performs in silico Legionella pneumophila sequence based typing. + legsta + legsta + legsta + Performs in silico Legionella pneumophila sequence based typing + Sequence analysis + Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta + https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta + 0.5.1 + legsta + 0.5.1 + (0/1) + (0/1) + (1/1) + (0/1) + False - lineagespot - 1.4.0 + lighter + 152.0 + 9.0 + lighter + Lighter is a kmer-based error correction method for whole genome sequencing data + lighter + lighter - r-base + Lighter + Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. + k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection + Sequencing, Whole genome sequencing, DNA, Genomics To update + https://github.com/mourisl/Lighter + Sequence Analysis, Fasta Manipulation + lighter + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/lighter + https://github.com/bgruening/galaxytools/tree/master/tools/lighter + 1.0 + lighter + 1.1.3 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + limma_voom + 20344.0 + 1012.0 + limma_voom + Perform RNA-Seq differential expression analysis using limma voom pipeline + limma + limma + + limma + Data analysis, linear models and differential expression for microarray data. + RNA-Seq analysis + Molecular biology, Genetics + Up-to-date + http://bioconductor.org/packages/release/bioc/html/limma.html + Transcriptomics, RNA, Statistics + limma_voom + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom + https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom + 3.58.1 + bioconductor-limma + 3.58.1 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + lineagespot + 37.0 + 2.0 lineagespot - Variant calling - Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) + lineagespot + lineagespot + + lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). + Variant calling + Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot + https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot + 1.6.0 + r-base + + (0/1) + (0/1) + (1/1) + (0/1) + False lorikeet - 20 - 20 - lorikeet - Up-to-date - - + lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + lorikeet + lorikeet + lorikeet + Tools for M. tuberculosis DNA fingerprinting (spoligotyping) + Sequence analysis, Genotyping + Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet + https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet + 20 + lorikeet + 20 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + lotus2 + 936.0 + 114.0 + lotus2 + LotuS2 OTU processing pipeline + lotus2 + lotus2 + + lotus2 + LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. + Sequence feature detection, DNA barcoding + Metagenomics, Taxonomy, Microbial ecology + Up-to-date + http://lotus2.earlham.ac.uk/ + Metagenomics + lotus2 + earlhaminst + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 + 2.32 + lotus2 + 2.32 + (0/1) + (0/1) + (1/1) + (0/1) + False m6anet - 2.1.0 - 2.1.0 + 3.0 + m6anet - Up-to-date + m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet + + m6Anet + Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning - m6anet to detect m6A RNA modifications from nanopore data - Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet + https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet + 2.1.0 + m6anet + 2.1.0 + (0/1) + (0/1) + (1/1) + (0/1) + False maaslin2 - 0.99.12 - 0.99.12 + 188.0 + 29.0 maaslin2 - Up-to-date - - - - MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. + maaslin2 + maaslin2 - Up-to-date + MaAsLin2 + MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. + Filtering, Statistical calculation, Standardisation and normalisation, Visualisation + Metagenomics, Statistics and probability + To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 + 0.99.12 + maaslin2 + 1.16.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + mafft + 143045.0 + 817.0 + rbc_mafft_add, rbc_mafft + Multiple alignment program for amino acid or nucleotide sequences + MAFFT + MAFFT + + MAFFT + MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. + Multiple sequence alignment + Sequence analysis + To update + https://mafft.cbrc.jp/alignment/software/ + RNA + mafft + rnateam + https://github.com/bgruening/galaxytools/tree/master/tools/mafft + https://github.com/bgruening/galaxytools/tree/master/tools/mafft + 7.520 + mafft + 7.525 + (2/2) + (2/2) + (2/2) + (2/2) + False + + + + make_nr + + + make_nr + Make a FASTA file non-redundant + + + + + + + + To update + https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr + Fasta Manipulation, Sequence Analysis + make_nr + peterjc + https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr + https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr + 0.0.2 + biopython + 1.70 + (0/1) + (0/1) + (0/1) + (0/1) + False maker - 2.31.11 - 3.01.03 + 4950.0 + 419.0 + maker, maker_map_ids + MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker - To update maker + MAKER + Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis - MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. - Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker + https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker + 2.31.11 + maker + 3.01.03 + (2/2) + (2/2) + (2/2) + (2/2) + False mapseq - 2.1.1 - - perl - To update - - - - + 167.0 + 2.0 + mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. + mapseq + mapseq + MAPseq + Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . + k-mer counting + Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq + 2.1.1 + perl + + (0/1) + (0/1) + (1/1) + (0/1) + False mash - 2.3 - 2.3 + 1739.0 + 12.0 + mash_screen, mash_sketch + Fast genome and metagenome distance estimation using MinHash mash - Up-to-date mash + Mash + Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation - Fast genome and metagenome distance estimation using MinHash - Fast genome and metagenome distance estimation using MinHash. Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash + 2.3 + mash + 2.3 + (2/2) + (2/2) + (2/2) + (2/2) + False maxbin2 - - 2.2.7 + 2059.0 + 118.0 maxbin2 - To update + clusters metagenomic contigs into bins + maxbin maxbin + MaxBin + Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology - clusters metagenomic contigs into bins - Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 + + maxbin2 + 2.2.7 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + maxquant + 5804.0 + 407.0 + maxquant, maxquant_mqpar + wrapper for MaxQuant + maxquant + maxquant + + MaxQuant + Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. + Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting + Proteomics experiment, Proteomics, Statistics and probability + Up-to-date + https://www.maxquant.org/ + Proteomics + maxquant + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant + 2.0.3.0 + maxquant + 2.0.3.0 + (2/2) + (2/2) + (2/2) + (0/2) + False mcl - 22.282 - 22.282 + 29.0 + 10.0 mcl - Up-to-date + The Markov Cluster Algorithm, a cluster algorithm for graphs mcl + mcl + MCL + MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks - The Markov Cluster Algorithm, a cluster algorithm for graphs - MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl + 22.282 + mcl + 22.282 + (0/1) + (0/1) + (1/1) + (0/1) + False medaka - 1.7.2 - 1.11.3 + + + medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant + Sequence correction provided by ONT Research medaka - To update medaka + Medaka + medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning - Sequence correction provided by ONT Research - medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka + https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka + 1.7.2 + medaka + 1.11.3 + (3/4) + (3/4) + (3/4) + (3/4) + False megahit - 1.2.9 - 1.2.9 + 9530.0 + 548.0 + megahit + An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit - Up-to-date megahit + MEGAHIT + Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly - An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. - Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit + https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit + 1.2.9 + megahit + 1.2.9 + (1/1) + (1/1) + (1/1) + (1/1) + False megahit_contig2fastg - 1.1.3 - 1.2.9 + 475.0 + 54.0 + megahit_contig2fastg + A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit - To update megahit + MEGAHIT + Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly - A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) - Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg + https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg + 1.1.3 + megahit + 1.2.9 + (1/1) + (0/1) + (1/1) + (0/1) + False megan - 6.21.7 - 6.24.20 + + + megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma + MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan - To update megan + MEGAN + Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis - MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). - Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan + https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan + 6.21.7 + megan + 6.25.9 + (0/7) + (0/7) + (7/7) + (0/7) + False meningotype - 0.8.5 - 0.8.5 - meningotype - Up-to-date - - + meningotype Assign sequence type to N. meningitidis genome assemblies + meningotype + meningotype + meningotype + In silico typing of Neisseria meningitidis contigs. + Genotyping, Multilocus sequence typing + Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype + https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype + 0.8.5 + meningotype + 0.8.5 + (0/1) + (0/1) + (0/1) + (0/1) + False merqury - 1.3 - 1.3 + 2483.0 + 244.0 + merqury, merquryplot + Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury - Up-to-date merqury + Merqury + Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology - Merqury is a tool for evaluating genomes assemblies based of k-mer operations. - Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury + https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury + 1.3 + merqury + 1.3 + (2/2) + (2/2) + (2/2) + (2/2) + False meryl - 1.3 - 1.3 - merqury - Up-to-date + 6785.0 + 350.0 + meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode + Meryl a k-mer counter. + meryl meryl + Meryl + Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing - Meryl a k-mer counter. - Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl + https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl + 1.3 + merqury + 1.3 + (0/7) + (0/7) + (0/7) + (0/7) + False metabat2 - 2.15 - 2.15 - metabat2 - Up-to-date + 4072.0 + 154.0 + metabat2_jgi_summarize_bam_contig_depths, metabat2 + MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 + MetaBAT_2 + MetaBAT 2 + an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing - MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. - an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 + 2.15 + metabat2 + 2.15 + (2/2) + (1/2) + (2/2) + (2/2) + False metaeuk - 5.34c21f2 - 6.a5d39d9 - metaeuk - To update + + + metaeuk_easy_predict + MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. + MetaEuk MetaEuk + MetaEuk + MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families - MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. - MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk + https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk + 5.34c21f2 + metaeuk + 6.a5d39d9 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + metagene_annotator + 636.0 + 115.0 + metagene_annotator + MetaGeneAnnotator gene-finding program for prokaryote and phage + metageneannotator + metageneannotator + + MetaGeneAnnotator + Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. + Sequence annotation + Genomics, Model organisms, Data submission, annotation and curation + Up-to-date + http://metagene.nig.ac.jp/ + Sequence Analysis + metagene_annotator + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator + 1.0 + metagene_annotator + 1.0 + (0/1) + (0/1) + (1/1) + (0/1) + False metagenomeseq - 1.16.0-0.0.1 - 1.43.0 - bioconductor-metagenomeseq - To update + + + metagenomeseq_normalizaton + metagenomeSeq Normalization + metagenomeseq metagenomeseq + metagenomeSeq + Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing - metagenomeSeq Normalization - Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq + 1.16.0-0.0.1 + bioconductor-metagenomeseq + 1.43.0 + (1/1) + (0/1) + (1/1) + (1/1) + False + + + + metanovo + 4181.0 + 15.0 + metanovo + Produce targeted databases for mass spectrometry analysis. + metanovo + metanovo + + MetaNovo + An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. + Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis + Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules + Up-to-date + https://github.com/uct-cbio/proteomics-pipelines + Proteomics + metanovo + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo + 1.9.4 + metanovo + 1.9.4 + (0/1) + (0/1) + (1/1) + (0/1) + False metaphlan - 4.0.6 - 4.0.6 + 10507.0 + 427.0 + customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan + MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan - Up-to-date metaphlan + MetaPhlAn + Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics - MetaPhlAn for Metagenomic Phylogenetic Analysis - Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. - Up-to-date + To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan + 4.0.6 + metaphlan + 4.1.1 + (1/4) + (2/4) + (4/4) + (4/4) + False + + + + metaquantome + + + metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz + quantitative analysis of microbiome taxonomy and function + metaQuantome + metaQuantome + + metaQuantome + metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. + Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference + Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics + Up-to-date + https://github.com/galaxyproteomics/metaquantome/ + Proteomics + metaquantome + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome + 2.0.2 + metaquantome + 2.0.2 + (0/6) + (6/6) + (6/6) + (0/6) + False + + + + metawrapmg + + + metawrapmg_binning + A flexible pipeline for genome-resolved metagenomic data analysis + metawrap + metawrap + + MetaWRAP + MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. + Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing + Whole genome sequencing, Metagenomic sequencing, Metagenomics + Up-to-date + https://github.com/bxlab/metaWRAP + Metagenomics + metawrapmg_binning + galaxy-australia + https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg + https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg + 1.3.0 + metawrap-mg + 1.3.0 + (0/1) + (1/1) + (1/1) + (0/1) + False minia - 3.2.6 - 3.2.6 + 2206.0 + 109.0 minia - Up-to-date + Short-read assembler based on a de Bruijn graph minia + minia + Minia + Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly - Short-read assembler based on a de Bruijn graph - Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia + https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia + 3.2.6 + minia + 3.2.6 + (0/1) + (1/1) + (1/1) + (0/1) + False miniasm - 0.3_r179 - 0.3 + 11938.0 + 178.0 miniasm - To update - - - - Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) + miniasm + miniasm + miniasm + Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. + De-novo assembly + Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm + https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm + 0.3_r179 + miniasm + 0.3 + (1/1) + (1/1) + (1/1) + (1/1) + False - miniprot - 0.12 - 0.12 - miniprot - Up-to-date - - + minipolish + 185.0 + 21.0 + minipolish + Polishing miniasm assemblies + minipolish + minipolish + minipolish + A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. + Localised reassembly, Read depth analysis + Sequence assembly, Sequencing + Up-to-date + https://github.com/rrwick/Minipolish + Sequence Analysis + minipolish + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/minipolish + https://github.com/bgruening/galaxytools/tree/master/tools/minipolish + 0.1.3 + minipolish + 0.1.3 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + miniprot + 813.0 + 15.0 + miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. + miniprot + miniprot + miniprot + Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. + Sequence alignment, Protein sequence analysis + Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot + https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot + 0.13 + miniprot + 0.13 + (0/2) + (0/2) + (2/2) + (2/2) + False mitos - 1.1.5 - 2.1.7 + 32022.0 + 58.0 + mitos, mitos2 + de-novo annotation of metazoan mitochondrial genomes mitos - To update mitos + MITOS + De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing - de-novo annotation of metazoan mitochondrial genomes - De novo metazoan mitochondrial genome annotation. To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos + 1.1.7 + mitos + 2.1.9 + (1/2) + (1/2) + (2/2) + (0/2) + False mlst - 2.22.0 - 2.23.0 + 9304.0 + 635.0 + mlst, mlst_list + Scan contig files against PubMLST typing schemes mlst - To update mlst + MLST - Taxonomic classification - Immunoproteins, genes and antigens - Scan contig files against PubMLST typing schemes Multi Locus Sequence Typing from an assembled genome or from a set of reads. + Multilocus sequence typing + Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst + 2.22.0 + mlst + 2.23.0 + (2/2) + (2/2) + (2/2) + (2/2) + False - mothur - 1.0 - 1.48.0 - mothur + mob_suite + 89021.0 + 322.0 + mob_recon, mob_typer + MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies + + + + + + + To update - mothur - mothur - DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis - Microbial ecology, Taxonomy, Sequence analysis, Phylogeny + https://github.com/phac-nml/mob-suite + Sequence Analysis + mob_suite + nml + https://github.com/phac-nml/mob-suite + https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite + 3.0.3 + mob_suite + 3.1.8 + (0/2) + (2/2) + (2/2) + (2/2) + False + + + + mothur + + + mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers + mothur + mothur + + mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities + DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis + Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur + 1.0 + mothur + 1.48.0 + (129/129) + (129/129) + (129/129) + (129/129) + False - multigsea - 1.8.0 - 1.12.0 - bioconductor-multigsea + mrbayes + + + mrbayes + A program for the Bayesian estimation of phylogeny. + + + + + + + + To update + + Sequence Analysis + mrbayes + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes + 1.0.2 + mrbayes + 3.2.7 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + msconvert + 20406.0 + 190.0 + msconvert + msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container + msconvert + msconvert + + msConvert + msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. + Filtering, Formatting + Proteomics, Proteomics experiment + To update + http://proteowizard.sourceforge.net/tools.shtml + Proteomics + msconvert + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert + 3.0.20287 + + + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + msstatstmt + 726.0 + 71.0 + msstatstmt + MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling + + + + + + + To update + http://msstats.org/msstatstmt/ + Proteomics + msstatstmt + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt + 2.0.0 + bioconductor-msstatstmt + 2.10.0 + (0/1) + (1/1) + (1/1) + (0/1) + False + + + + multigsea + 53.0 + 2.0 + multigsea + GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA + + multiGSEA + A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules - GSEA-based pathway enrichment analysis for multi-omics data - A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. - To update + Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea + 1.12.0 + bioconductor-multigsea + 1.12.0 + (0/1) + (0/1) + (1/1) + (0/1) + False multiqc - 1.11 - 1.19 + 162790.0 + 8320.0 + multiqc + MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc - To update multiqc + MultiQC - Validation - Sequencing, Bioinformatics - MultiQC aggregates results from bioinformatics analyses across many samples into a single report MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + Validation, Sequencing quality control + Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc + 1.11 + multiqc + 1.22.2 + (1/1) + (1/1) + (1/1) + (1/1) + False mykrobe - 0.10.0 - 0.13.0 - mykrobe - To update + + + mykrobe_predict + Antibiotic resistance predictions + Mykrobe Mykrobe + Mykrobe + Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics - Antibiotic resistance predictions - Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe + https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe + 0.10.0 + mykrobe + 0.13.0 + (0/1) + (0/1) + (0/1) + (0/1) + False - nanocompore - 1.0.0rc3.post2 - 1.0.4 - nanocompore + mykrobe_parser + + + mykrobe_parseR + RScript to parse the results of mykrobe predictor. + + + + + + + + To update + https://github.com/phac-nml/mykrobe-parser + Sequence Analysis + mykrobe_parser + nml + https://github.com/phac-nml/mykrobe-parser + https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser + 0.1.4.1 + r-base + + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + mz_to_sqlite + 844.0 + 33.0 + mz_to_sqlite + Creates a SQLite database for proteomics data + mztosqlite + mztosqlite + + mzToSQLite + Convert proteomics data files into a SQLite database + Conversion, Peptide database search + Proteomics, Biological databases To update + https://github.com/galaxyproteomics/mzToSQLite + Proteomics + mz_to_sqlite + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite + 2.1.1+galaxy0 + mztosqlite + 2.1.1 + (1/1) + (1/1) + (1/1) + (0/1) + False + + + + nanocompore + + + nanocompore_db, nanocompore_sampcomp + Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. + Nanocompore Nanocompore + Nanocompore + RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites - Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. - RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore + 1.0.0rc3.post2 + nanocompore + 1.0.4 + (0/2) + (1/2) + (2/2) + (0/2) + False + + + + nanoplot + 63235.0 + 2195.0 + nanoplot + Plotting tool for long read sequencing data and alignments + nanoplot + nanoplot + + NanoPlot + NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences + Scatter plot plotting, Box-Whisker plot plotting + Genomics + Up-to-date + https://github.com/wdecoster/NanoPlot + Visualization + nanoplot + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot + 1.42.0 + nanoplot + 1.42.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + nanopolishcomp + + + nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate + NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. + nanopolishcomp + nanopolishcomp + + NanopolishComp + NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. + Methylation analysis, Collapsing methods + Sequence analysis, Sequencing, Genetic variation + To update + https://a-slide.github.io/NanopolishComp + Sequence Analysis + nanopolishcomp + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp + 0.6.11 + nanopolishcomp + 0.6.12 + (0/2) + (0/2) + (2/2) + (2/2) + False + + + + ncbi_blast_plus + 365597.0 + 4066.0 + blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper + NCBI BLAST+ + + + + + + + + To update + https://blast.ncbi.nlm.nih.gov/ + Sequence Analysis + ncbi_blast_plus + devteam + https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus + https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus + 2.14.1 + python + + (16/18) + (16/18) + (16/18) + (16/18) + False + + + + ncbi_fcs_gx + + + ncbi_fcs_gx + FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). + ncbi_fcs + ncbi_fcs + + NCBI fcs + The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. + Sequence assembly validation, Sequence trimming, Sequence contamination filtering + Sequence analysis, Sequence assembly + Up-to-date + https://github.com/ncbi/fcs-gx + Sequence Analysis + ncbi_fcs_gx + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx + https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx + 0.5.0 + ncbi-fcs-gx + 0.5.0 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + newick_utils + 25505.0 + 448.0 + newick_display + Perform operations on Newick trees + newick_utilities + newick_utilities + + Newick Utilities + The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. + Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction + Phylogeny, Genomics, Computer science + To update + http://cegg.unige.ch/newick_utils + Visualization, Metagenomics + newick_utils + iuc + https://github.com/tjunier/newick_utils + https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils + 1.6+galaxy1 + newick_utils + 1.6 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + nextclade + 3527.0 + 169.0 + nextalign, nextclade + Identify differences between your sequences and a reference sequence used by Nextstrain + nextclade + nextclade + + Nextclade + Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. + Methylation analysis, Variant calling + Genomics, Sequence analysis, Cladistics + To update + https://github.com/nextstrain/nextclade + Sequence Analysis + + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade + 2.7.0 + nextalign + 2.14.0 + (1/2) + (1/2) + (2/2) + (2/2) + False + + + + nextdenovo + 268.0 + 84.0 + nextdenovo + String graph-based de novo assembler for long reads + nextdenovo + nextdenovo + + NextDenovo + NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. + De-novo assembly, Genome assembly + Sequencing, Sequence assembly + To update + https://github.com/Nextomics/NextDenovo + Assembly + nextdenovo + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo + https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo + 2.5.0 + nextdenovo + 2.5.2 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + nonpareil + 142.0 + 5.0 + nonpareil + Estimate average coverage in metagenomic datasets + nonpareil + nonpareil + + nonpareil + Estimate metagenomic coverage and sequence diversity + Operation + + To update + http://nonpareil.readthedocs.io + Metagenomics + nonpareil + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil + 3.1.1 + nonpareil + 3.4.1 + (1/1) + (0/1) + (1/1) + (1/1) + False + + + + nucleosome_prediction + 861.0 + 2.0 + Nucleosome + Prediction of Nucleosomes Positions on the Genome + nucleosome_prediction + nucleosome_prediction + + nucleosome_prediction + Prediction of Nucleosomes Positions on the Genome + Prediction and recognition, Nucleosome position prediction, Sequence analysis + Structural genomics, Nucleic acid sites, features and motifs + Up-to-date + https://genie.weizmann.ac.il/software/nucleo_exe.html + Sequence Analysis + nucleosome_prediction + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction + https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction + 3.0 + nucleosome_prediction + 3.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + nugen_nudup + + + nugen_nudup + Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. + nudup + nudup + + NuDup + Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. + Duplication detection + Sequencing + Up-to-date + https://github.com/tecangenomics/nudup + SAM, Metagenomics, Sequence Analysis, Transcriptomics + nugen_nudup + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup + https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup + 2.3.3 + nudup + 2.3.3 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + obisindicators + 45.0 + 4.0 + obisindicators, obis_data + Compute biodiveristy indicators for marine data from obis + + + + + + + + To update + https://github.com/Marie59/obisindicators + Ecology + + ecology + https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators + https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators + 0.0.2 + r-base + + (1/2) + (0/2) + (2/2) + (1/2) + False + + + + obitools + + + obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq + OBITools is a set of programs developed to simplify the manipulation of sequence files + obitools + obitools + + OBITools + Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. + Sequence analysis, Sequence analysis + Sequence analysis, DNA, Sequencing + Up-to-date + http://metabarcoding.org/obitools + Sequence Analysis + obitools + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools + https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools + 1.2.13 + obitools + 1.2.13 + (0/10) + (10/10) + (10/10) + (10/10) + False + + + + omark + + + omark + Proteome quality assessment software + omark + omark + + OMArk + Proteome quality assessment software + Sequence assembly validation, Differential protein expression profiling + Proteomics, Sequence analysis, Statistics and probability + To update + https://github.com/DessimozLab/OMArk + Sequence Analysis + omark + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark + 0.3.0 + + + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + orfipy + 774.0 + 53.0 + orfipy + Galaxy wrapper for ORFIPY + orfipy + orfipy + + orfipy + A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. + Coding region prediction, Database search, Transcriptome assembly, De-novo assembly + Computer science, RNA-Seq, Transcriptomics, Small molecules + Up-to-date + https://github.com/urmi-21/orfipy + Sequence Analysis + orfipy + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy + https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy + 0.0.4 + orfipy + 0.0.4 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + orthofinder + + + orthofinder_onlygroups + Accurate inference of orthologous gene groups made easy + OrthoFinder + OrthoFinder + + OrthoFinder + OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. + Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment + Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis + Up-to-date + https://github.com/davidemms/OrthoFinder + Phylogenetics, Sequence Analysis + orthofinder + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder + https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder + 2.5.5 + orthofinder + 2.5.5 + (0/1) + (1/1) + (1/1) + (1/1) + False + + + + peptideshaker + 17477.0 + 485.0 + fasta_cli, ident_params, peptide_shaker, search_gui + PeptideShaker and SearchGUI + + + + + + + + To update + http://compomics.github.io + Proteomics + peptideshaker + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker + + searchgui + 4.3.6 + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + pfamscan + 165.0 + 19.0 + pfamscan + Search a FASTA sequence against a library of Pfam HMM. + pfamscan + pfamscan + + PfamScan + This tool is used to search a FASTA sequence against a library of Pfam HMM. + Protein sequence analysis + Sequence analysis + Up-to-date + http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ + Sequence Analysis + pfamscan + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan + https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan + 1.6 + pfam_scan + 1.6 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + pharokka + 2565.0 + 74.0 + pharokka + rapid standardised annotation tool for bacteriophage genomes and metagenomes + pharokka + pharokka + + Pharokka + Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. + Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly + Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA + To update + https://github.com/gbouras13/pharokka + Genome annotation + pharokka + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + 1.3.2 + \n pharokka\n + + (0/1) + (1/1) + (1/1) + (0/1) + False + + + + phyloseq + + + phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness + Handling and analysis of high-throughput microbiome census data + phyloseq + phyloseq + + phyloseq + Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. + Deposition, Analysis, Visualisation + Microbiology, Sequence analysis, Metagenomics + Up-to-date + https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html + Metagenomics + phyloseq + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq + 1.46.0 + bioconductor-phyloseq + 1.46.0 + (0/4) + (0/4) + (4/4) + (0/4) + False + + + + phyml + 1770.0 + 104.0 + phyml + PhyML is a phylogeny software based on the maximum-likelihood principle. + phyml + phyml + + PhyML + Phylogenetic estimation software using Maximum Likelihood + Phylogenetic tree generation (maximum likelihood and Bayesian methods) + Phylogenetics, Bioinformatics, Phylogenetics + Up-to-date + http://www.atgc-montpellier.fr/phyml/ + Phylogenetics + phyml + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml + https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml + 3.3.20220408 + phyml + 3.3.20220408 + (0/1) + (1/1) + (1/1) + (1/1) + False + + + + picrust + + + picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes + PICRUSt wrappers + picrust + picrust + + PICRUSt + PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. + Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding + Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing + To update + https://picrust.github.io/picrust/ + Metagenomics + picrust + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust + https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust + 1.1.1 + picrust + 1.1.4 + (0/6) + (6/6) + (5/6) + (6/6) + False + + + + picrust2 + + + picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions + PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States + picrust2 + picrust2 + + PICRUSt2 + PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis + Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing + To update + https://github.com/picrust/picrust2/wiki + Metagenomics + picrust2 + iuc + https://github.com/picrust/picrust2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 + 2.5.1 + picrust2 + 2.5.2 + (0/7) + (7/7) + (7/7) + (0/7) + False + + + + plasflow + 22589.0 + 278.0 + PlasFlow + PlasFlow - Prediction of plasmid sequences in metagenomic contigs. + plasflow + plasflow + + PlasFlow + PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. + Sequence analysis + Metagenomics + Up-to-date + https://github.com/smaegol/PlasFlow + Sequence Analysis + plasflow + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow + https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow + 1.1.0 + plasflow + 1.1.0 + (1/1) + (1/1) + (1/1) + (0/1) + False + + + + plasmidfinder + 22.0 + 8.0 + plasmidfinder + "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" + PlasmidFinder + PlasmidFinder + + PlasmidFinder + PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). + Genome assembly, Scaffolding, Multilocus sequence typing + Whole genome sequencing, Sequence assembly, Mapping, Probes and primers + Up-to-date + https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ + Sequence Analysis + plasmidfinder + iuc + https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder + https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder + 2.1.6 + plasmidfinder + 2.1.6 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + plasmidspades + + + plasmidspades + Genome assembler for assemblying plasmid + + + + + + + + To update + + Assembly + plasmidspades + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades + 1.1 + spades + 3.15.5 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + polypolish + 239.0 + 24.0 + polypolish + "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." + Polypolish + Polypolish + + Polypolish + Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. + Genome assembly, Read mapping, Mapping assembly, Sequencing error detection + Sequence assembly, Sequence composition, complexity and repeats, Mapping + To update + https://github.com/rrwick/Polypolish + Sequence Analysis + polypolish + iuc + https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish + https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish + 0.5.0 + polypolish + 0.6.0 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + prodigal + + + prodigal + A protein-coding gene prediction software tool for bacterial and archaeal genomes + prodigal + prodigal + + Prodigal + Fast, reliable protein-coding gene prediction for prokaryotic genomes. + Genome annotation + Genomics, Sequence analysis + Up-to-date + https://github.com/hyattpd/Prodigal + Genome annotation + prodigal + iuc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal + https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal + 2.6.3 + prodigal + 2.6.3 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + prokka + 371445.0 + 3233.0 + prokka + Rapid annotation of prokaryotic genomes + prokka + prokka + + Prokka + Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. + Gene prediction, Coding region prediction, Genome annotation + Genomics, Model organisms, Virology + Up-to-date + http://github.com/tseemann/prokka + Sequence Analysis + prokka + crs4 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka + 1.14.6 + prokka + 1.14.6 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + promer + + + promer4_substitutions + Aligns two sets of contigs and reports amino acid substitutions between them + + + + + + + + To update + https://github.com/phac-nml/promer + Assembly + promer + nml + https://github.com/phac-nml/promer + https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer + 1.2 + python + + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + proteinortho + 2092.0 + 125.0 + proteinortho, proteinortho_grab_proteins, proteinortho_summary + Proteinortho is a tool to detect orthologous proteins/genes within different species. + proteinortho + proteinortho + + Proteinortho + Proteinortho is a tool to detect orthologous genes within different species + Sequence clustering, Sequence analysis + Comparative genomics + Up-to-date + https://gitlab.com/paulklemm_PHD/proteinortho + Proteomics + proteinortho + iuc + https://gitlab.com/paulklemm_PHD/proteinortho + https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho + 6.3.1 + proteinortho + 6.3.1 + (0/3) + (0/3) + (3/3) + (0/3) + False + + + + pycoqc + 21123.0 + 350.0 + pycoqc + QC metrics for ONT Basecalling + pycoqc + pycoqc + + pycoQC + PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. + Sequencing quality control, Statistical calculation + Sequence analysis, Data quality management, Sequencing + Up-to-date + https://github.com/tleonardi/pycoQC + Nanopore + pycoqc + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc + 2.5.2 + pycoqc + 2.5.2 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + pygenometracks + 11332.0 + 377.0 + pygenomeTracks + pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. + pygenometracks + pygenometracks + + pyGenomeTracks + reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. + Visualisation, Formatting + Model organisms, Imaging, Workflows + To update + https://github.com/deeptools/pyGenomeTracks + Visualization + pygenometracks + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks + https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks + 3.8 + pygenometracks + 3.9 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + qiime_add_on + + + qiime_collapse_samples, qiime_make_otu_table + QIIME to perform microbial community analysis + qiime_add_on + qiime_add_on + + qiime_add_on + QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. + Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control + Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics + To update + http://www.qiime.org + Metagenomics + qiime + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on + + qiime + 1.9.1 + (0/2) + (0/2) + (2/2) + (2/2) + False + + + + qiime_core + + + qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file + QIIME to perform microbial community analysis + + + + + + + + To update + http://www.qiime.org + Metagenomics + qiime + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core + + qiime + 1.9.1 + (0/32) + (0/32) + (32/32) + (32/32) + False + + + + qualimap + + + qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq + + qualimap + qualimap + + QualiMap + Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. + Sequencing quality control + Data quality management + To update + http://qualimap.bioinfo.cipf.es/ + Sequence Analysis, Transcriptomics, SAM + qualimap + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap + https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap + 2.2.2d + qualimap + 2.3 + (4/4) + (4/4) + (4/4) + (1/4) + False + + + + quast + 51567.0 + 3567.0 + quast + Quast (Quality ASsessment Tool) evaluates genome assemblies. + quast + quast + + QUAST + QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. + Visualisation, Sequence assembly validation + Sequence assembly + Up-to-date + http://quast.bioinf.spbau.ru/ + Assembly + quast + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast + https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast + 5.2.0 + quast + 5.2.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + quickmerge + + + quickmerge + Merge long-read and hybrid assemblies to increase contiguity + quickmerge + quickmerge + + quickmerge + Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. + Genome assembly, Scaffolding, De-novo assembly, Genotyping + Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype + Up-to-date + https://github.com/mahulchak/quickmerge + Assembly + quickmerge + galaxy-australia + https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge + https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge + 0.3 + quickmerge + 0.3 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + rRNA + + + meta_rna + Identification of ribosomal RNA genes in metagenomic fragments. + + + + + + + + To update + http://weizhong-lab.ucsd.edu/meta_rna/ + RNA + rrna + rnateam + https://github.com/bgruening/galaxytools/tree/master/tools/rRNA + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA + 0.1 + hmmsearch3.0 + + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + racon + 21353.0 + 309.0 + racon + Consensus module for raw de novo DNA assembly of long uncorrected reads. + Racon + Racon + + Racon + Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. + Genome assembly, Mapping assembly + Whole genome sequencing, Sequence assembly + Up-to-date + https://github.com/isovic/racon + Sequence Analysis + racon + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/racon + https://github.com/bgruening/galaxytools/tree/master/tools/racon + 1.5.0 + racon + 1.5.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + rasusa + + + rasusa + Randomly subsample sequencing reads to a specified coverage + rasusa + rasusa + + rasusa + Produces an unbiased subsample of your reads + + + To update + https://github.com/mbhall88/rasusa + Sequence Analysis + rasusa + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa + https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa + 0.8.0 + rasusa + 2.0.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + raxml + 6808.0 + 383.0 + raxml + RAxML - A Maximum Likelihood based phylogenetic inference + raxml + raxml + + RAxML + A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + Sequence analysis, Phylogenetic tree analysis + Phylogenetics, Sequence analysis + To update + http://www.exelixis-lab.org/web/software/raxml/ + Phylogenetics + raxml + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml + https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml + 8.2.12 + raxml + 8.2.13 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + read_it_and_keep + 3370.0 + 71.0 + read_it_and_keep + Rapid decontamination of SARS-CoV-2 sequencing reads + read_it_and_keep + read_it_and_keep + + read_it_and_keep + Read contamination removal + Filtering, Genome alignment + Pathology, Genomics + To update + https://github.com/GenomePathogenAnalysisService/read-it-and-keep + Sequence Analysis + read_it_and_keep + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep + https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep + 0.2.2 + read-it-and-keep + 0.3.0 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + reago + + + reago + Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. + reago + reago + + REAGO + This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. + Sequence assembly + Sequence assembly, RNA, Metagenomics, Microbiology + Up-to-date + https://github.com/chengyuan/reago-1.1 + Metagenomics, RNA + reago + rnateam + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago + 1.1 + reago + 1.1 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + recentrifuge + 331.0 + 48.0 + recentrifuge + "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." + Recentrifuge + Recentrifuge + + Recentrifuge + Robust comparative analysis and contamination removal for metagenomics. + Taxonomic classification, Expression analysis, Cross-assembly + Metagenomics, Microbial ecology, Metagenomic sequencing + Up-to-date + https://github.com/khyox/recentrifuge + Metagenomics + recentrifuge + iuc + https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge + https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge + 1.14.0 + recentrifuge + 1.14.0 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + repeatexplorer2 + + + repeatexplorer_clustering + Tool for annotation of repeats from unassembled shotgun reads. + + + + + + + + To update + https://github.com/repeatexplorer/repex_tarean + Genome annotation + repeatexplorer2 + gga + https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 + https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 + 2.3.8 + + + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + roary + 12225.0 + 656.0 + roary + Roary the pangenome pipeline + roary + roary + + Roary + A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. + Genome assembly + DNA, Genomics, Mapping + Up-to-date + https://sanger-pathogens.github.io/Roary/ + Sequence Analysis + roary + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary + https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary + 3.13.0 + roary + 3.13.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + rseqc + 135036.0 + 3269.0 + rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin + an RNA-seq quality control package + rseqc + rseqc + + RSeQC + Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. + Data handling + Sequencing + Up-to-date + https://code.google.com/p/rseqc/ + Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization + rseqc + nilesh + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc + https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc + 5.0.3 + rseqc + 5.0.3 + (22/22) + (22/22) + (22/22) + (22/22) + False + + + + salmon + 55161.0 + 746.0 + alevin, salmon, salmonquantmerge + Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. + salmon + salmon + + Salmon + A tool for transcript expression quantification from RNA-seq data + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis + RNA-Seq, Gene expression, Transcriptomics + To update + https://github.com/COMBINE-lab/salmon + Sequence Analysis, RNA, Transcriptomics + + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + 1.10.1 + salmon + 1.10.3 + (2/3) + (1/3) + (3/3) + (1/3) + False + + + + sarscov2formatter + 173.0 + 7.0 + sarscov2formatter + sarscov2formatter custom script + + + + + + + + Up-to-date + https://github.com/nickeener/sarscov2formatter + Sequence Analysis + sarscov2formatter + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter + https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter + 1.0 + sarscov2formatter + 1.0 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + sarscov2summary + 140.0 + 1.0 + sarscov2summary + sarscov2summary custom script + + + + + + + + To update + https://github.com/nickeener/sarscov2summary + Sequence Analysis + sarscov2summary + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary + https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary + 0.1 + sarscov2summary + 0.5 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + scoary + 676.0 + 61.0 + scoary + Scoary calculates the assocations between all genes in the accessory genome and the traits. + scoary + scoary + + Scoary + Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. + Analysis + Genotype and phenotype, Model organisms, GWAS study, Functional genomics + Up-to-date + https://github.com/AdmiralenOla/Scoary + Metagenomics + scoary + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary + https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary + 1.6.16 + scoary + 1.6.16 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + semibin + 183.0 + 10.0 + semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train + SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks + semibin + semibin + + SemiBin + Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. + Sequence assembly, Read binning + Metagenomics, Machine learning, Microbial ecology, Sequence assembly + To update + https://semibin.readthedocs.io/en/latest/ + Metagenomics + semibin + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin + https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin + 2.0.2 + semibin + 2.1.0 + (0/6) + (0/6) + (6/6) + (1/6) + False + + + + seqkit + + + seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate + A cross-platform and ultrafast toolkit for FASTA/Q file manipulation + seqkit + seqkit + + seqkit + FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. + DNA transcription, Sequence trimming, DNA translation, Sequence conversion + Database management, Sequence analysis + Up-to-date + https://bioinf.shenwei.me/seqkit/ + Sequence Analysis + seqkit + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit + https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit + 2.8.2 + seqkit + 2.8.2 + (0/5) + (2/5) + (3/5) + (2/5) + False + + + + seqprep + + + seqprep + Tool for merging paired-end Illumina reads and trimming adapters. + seqprep + seqprep + + SeqPrep + Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. + Nucleic acid design + Genomics, Sequence assembly, Sequencing, Probes and primers + Up-to-date + https://github.com/jstjohn/SeqPrep + Fastq Manipulation, Sequence Analysis + seqprep + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep + https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep + 1.3.2 + seqprep + 1.3.2 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + seqsero2 + 12.0 + + seqsero2 + Salmonella serotype prediction from genome sequencing data + seqsero2 + seqsero2 + + SeqSero2 + rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) + Genome indexing, Antimicrobial resistance prediction, Genome alignment + Whole genome sequencing, Sequence assembly, Genomics + Up-to-date + https://github.com/denglab/SeqSero2 + Sequence Analysis + seqsero2 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 + 1.3.1 + seqsero2 + 1.3.1 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + shorah + + + shorah_amplicon + Reconstruct haplotypes using ShoRAH in amplicon mode + shorah + shorah + + ShoRAH + Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. + Haplotype mapping, Variant calling + Metagenomics, Sequencing, Genetics + To update + https://github.com/cbg-ethz/shorah/blob/master/README.md + Sequence Analysis + shorah_amplicon + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah + https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah + 1.1.3 + shorah + 1.99.2 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + shovill + 41600.0 + 1008.0 + shovill + Faster de novo assembly pipeline based around Spades + shovill + shovill + + shovill + Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. + Genome assembly + Genomics, Microbiology, Sequence assembly + Up-to-date + https://github.com/tseemann/shovill + Assembly + shovill + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill + https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill + 1.1.0 + shovill + 1.1.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + sistr_cmd + 2489.0 + 133.0 + sistr_cmd + SISTR in silico serotyping tool + + + + + + + + To update + https://github.com/phac-nml/sistr_cmd + Sequence Analysis + sistr_cmd + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd + 1.1.1 + sistr_cmd + 1.1.2 + (0/1) + (1/1) + (1/1) + (0/1) + False + + + + smallgenomeutilities + + + smgu_frameshift_deletions_checks + Set of utilities for manipulating small viral genome data. + v-pipe + v-pipe + + V-pipe + Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. + Read pre-processing, Sequence alignment, Genetic variation analysis + Genomics, Population genetics, Workflows, Virology, Sequencing + To update + https://github.com/cbg-ethz/smallgenomeutilities + Sequence Analysis + smallgenomeutilities + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities + https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities + 0.4.0 + smallgenomeutilities + 0.4.1 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + smalt + + + smalt + SMALT aligns DNA sequencing reads with a reference genome. + + + + + + + + Up-to-date + http://www.sanger.ac.uk/science/tools/smalt-0 + Sequence Analysis + smalt + nml + https://sourceforge.net/projects/smalt/ + https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt + 0.7.6 + smalt + 0.7.6 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + snap + + + snap, snap_training + SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. + snap + snap + + SNAP + The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. + Gene prediction + DNA, DNA polymorphism, Genetics + Up-to-date + https://github.com/KorfLab/SNAP + Sequence Analysis + snap + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap + https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap + 2013_11_29 + snap + 2013_11_29 + (1/2) + (1/2) + (1/2) + (0/2) + False + + + + snippy + 105708.0 + 1372.0 + snippy_core, snippy, snippy_clean_full_aln + Contains the snippy tool for characterising microbial snps + snippy + snippy + + snippy + Rapid haploid variant calling and core SNP phylogeny generation. + Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling + Genomics, Model organisms, DNA polymorphism, Phylogenetics + To update + https://github.com/tseemann/snippy + Sequence Analysis + snippy + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy + https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy + + snippy + 4.6.0 + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + sonneityping + 1.0 + 1.0 + sonneityping + Scripts for parsing Mykrobe predict results for Shigella sonnei. + sonneityping + sonneityping + + sonneityping + Scripts for parsing Mykrobe predict results for Shigella sonnei. + Antimicrobial resistance prediction, Variant calling, Genotyping + Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics + Up-to-date + https://github.com/katholt/sonneityping + Sequence Analysis + sonneityping + iuc + https://github.com/katholt/sonneityping + https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping + 20210201 + sonneityping + 20210201 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + sortmerna + 18504.0 + 376.0 + bg_sortmerna + SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. + sortmerna + sortmerna + + SortMeRNA + Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. + Sequence similarity search, Sequence comparison, Sequence alignment analysis + Metatranscriptomics, Metagenomics + Up-to-date + http://bioinfo.lifl.fr/RNA/sortmerna/ + RNA + sortmerna + rnateam + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna + https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna + 4.3.6 + sortmerna + 4.3.6 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + spades + 58834.0 + 2309.0 + spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades + SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. + spades + rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades + + SPAdes + St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. + Genome assembly + Sequence assembly + Up-to-date + https://github.com/ablab/spades + Assembly, RNA, Metagenomics + spades + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades + https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades + 3.15.5 + spades + 3.15.5 + (9/9) + (9/9) + (9/9) + (9/9) + False + + + + spotyping + 1278.0 + 12.0 + spotyping + SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads + spotyping + spotyping + + SpoTyping + Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. + Variant pattern analysis + Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation + Up-to-date + https://github.com/xiaeryu/SpoTyping-v2.0 + Sequence Analysis + spotyping + iuc + https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine + https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping + 2.1 + spotyping + 2.1 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + sr_bowtie + + + bowtieForSmallRNA + bowtie wrapper tool to align small RNA sequencing reads + + + + + + + + To update + http://artbio.fr + RNA, Next Gen Mappers + sr_bowtie + artbio + https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie + https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie + 2.3.0 + bowtie + 1.3.1 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + srst2 + 205.0 + 22.0 + srst2 + SRST2 Short Read Sequence Typing for Bacterial Pathogens + srst2 + srst2 + + srst2 + Short Read Sequence Typing for Bacterial Pathogens + Multilocus sequence typing + Whole genome sequencing, Public health and epidemiology + To update + http://katholt.github.io/srst2/ + Metagenomics + srst2 + iuc + https://github.com/katholt/srst2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 + 0.2.0 + samtools + 1.20 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + srst2 + 205.0 + 22.0 + srst2 + Short Read Sequence Typing for Bacterial Pathogens + + + + + + + + To update + + Sequence Analysis + srst2 + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 + 0.3.7 + srst2 + 0.2.0 + (0/1) + (0/1) + (1/1) + (0/1) + False + + + + staramr + 12673.0 + 889.0 + staramr_search + Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. + + + + + + + + Up-to-date + https://github.com/phac-nml/staramr + Sequence Analysis + staramr + nml + https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr + https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr + 0.10.0 + staramr + 0.10.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + stringmlst + + + stringmlst + Rapid and accurate identification of the sequence type (ST) + + + + + + + + To update + + Sequence Analysis + stringmlst + nml + + https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst + 1.1.0 + stringMLST + 0.6.3 + (0/1) + (0/1) + (0/1) + (0/1) + False + + + + structure + 2623.0 + 59.0 + structure + for using multi-locus genotype data to investigate population structure. + structure + structure + + Structure + The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. + Genetic variation analysis + Population genetics + Up-to-date + + Phylogenetics, Variant Analysis + structure + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure + https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure + 2.3.4 + structure + 2.3.4 + (0/1) + (0/1) + (1/1) + (1/1) + False + + + + suite_qiime2__alignment + + + qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask + + + + + + + + + To update + https://github.com/qiime2/q2-alignment + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__alignment + + + qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask + + + + + + + + + To update + https://github.com/qiime2/q2-alignment + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__alignment + + + qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask + + + + + + + + + To update + https://github.com/qiime2/q2-alignment + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__alignment + + + qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask + + + + + + + + + To update + https://github.com/qiime2/q2-alignment + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__composition + + + qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-composition + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + 2024.2.0+q2galaxy.2024.2.1 + + + (4/5) + (4/5) + (4/5) + (2/5) + False + + + + suite_qiime2__composition + + + qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-composition + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + 2024.2.0+q2galaxy.2024.2.1 + + + (4/5) + (4/5) + (4/5) + (2/5) + False + + + + suite_qiime2__composition + + + qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-composition + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + 2024.2.0+q2galaxy.2024.2.1 + + + (4/5) + (4/5) + (4/5) + (2/5) + False + + + + suite_qiime2__composition + + + qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-composition + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition + 2024.2.0+q2galaxy.2024.2.1 + + + (4/5) + (4/5) + (4/5) + (2/5) + False + + + + suite_qiime2__cutadapt + + + qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single + + + + + + + + + To update + https://github.com/qiime2/q2-cutadapt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__cutadapt + + + qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single + + + + + + + + + To update + https://github.com/qiime2/q2-cutadapt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__cutadapt + + + qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single + + + + + + + + + To update + https://github.com/qiime2/q2-cutadapt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__cutadapt + + + qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single + + + + + + + + + To update + https://github.com/qiime2/q2-cutadapt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__dada2 + + + qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single + + + + + + + + + To update + http://benjjneb.github.io/dada2/ + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__dada2 + + + qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single + + + + + + + + + To update + http://benjjneb.github.io/dada2/ + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__dada2 + + + qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single + + + + + + + + + To update + http://benjjneb.github.io/dada2/ + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__dada2 + + + qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single + + + + + + + + + To update + http://benjjneb.github.io/dada2/ + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False + + + + suite_qiime2__deblur + + + qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats + + + + + + + + + To update + https://github.com/biocore/deblur + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__deblur + + + qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats + + + + + + + + + To update + https://github.com/biocore/deblur + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__deblur + + + qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats + + + + + + + + + To update + https://github.com/biocore/deblur + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__deblur + + + qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats + + + + + + + + + To update + https://github.com/biocore/deblur + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__demux + + + qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts + + + + + + + + + To update + https://github.com/qiime2/q2-demux + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + 2024.2.0+q2galaxy.2024.2.1 + + + (6/9) + (6/9) + (6/9) + (6/9) + False + + + + suite_qiime2__demux + + + qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts + + + + + + + + + To update + https://github.com/qiime2/q2-demux + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + 2024.2.0+q2galaxy.2024.2.1 + + + (6/9) + (6/9) + (6/9) + (6/9) + False + + + + suite_qiime2__demux + + + qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts + + + + + + + + + To update + https://github.com/qiime2/q2-demux + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + 2024.2.0+q2galaxy.2024.2.1 + + + (6/9) + (6/9) + (6/9) + (6/9) + False + + + + suite_qiime2__demux + + + qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts + + + + + + + + + To update + https://github.com/qiime2/q2-demux + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux + 2024.2.0+q2galaxy.2024.2.1 + + + (6/9) + (6/9) + (6/9) + (6/9) + False + + + + suite_qiime2__diversity + + + qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap + + + + + + + + + To update + https://github.com/qiime2/q2-diversity + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + 2024.2.0+q2galaxy.2024.2.1 + + + (21/22) + (21/22) + (21/22) + (21/22) + False + + + + suite_qiime2__diversity + + + qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap + + + + + + + + + To update + https://github.com/qiime2/q2-diversity + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + 2024.2.0+q2galaxy.2024.2.1 + + + (21/22) + (21/22) + (21/22) + (21/22) + False + + + + suite_qiime2__diversity + + + qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap + + + + + + + + + To update + https://github.com/qiime2/q2-diversity + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + 2024.2.0+q2galaxy.2024.2.1 + + + (21/22) + (21/22) + (21/22) + (21/22) + False + + + + suite_qiime2__diversity + + + qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap + + + + + + + + + To update + https://github.com/qiime2/q2-diversity + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity + 2024.2.0+q2galaxy.2024.2.1 + + + (21/22) + (21/22) + (21/22) + (21/22) + False + + + + suite_qiime2__diversity_lib + + + qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac + + + + + + + + + To update + https://github.com/qiime2/q2-diversity-lib + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__diversity_lib + + + qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac + + + + + + + + + To update + https://github.com/qiime2/q2-diversity-lib + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__diversity_lib + + + qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac + + + + + + + + + To update + https://github.com/qiime2/q2-diversity-lib + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__diversity_lib + + + qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac + + + + + + + + + To update + https://github.com/qiime2/q2-diversity-lib + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__emperor + + + qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot + + + + + + + + + To update + http://emperor.microbio.me + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__emperor + + + qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot + + + + + + + + + To update + http://emperor.microbio.me + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__emperor + + + qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot + + + + + + + + + To update + http://emperor.microbio.me + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__emperor + + + qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot + + + + + + + + + To update + http://emperor.microbio.me + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__feature_classifier + + + qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global + + + + + + + + + To update + https://github.com/qiime2/q2-feature-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (10/11) + (10/11) + (10/11) + (10/11) + False + + + + suite_qiime2__feature_classifier + + + qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global + + + + + + + + + To update + https://github.com/qiime2/q2-feature-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (10/11) + (10/11) + (10/11) + (10/11) + False + + + + suite_qiime2__feature_classifier + + + qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global + + + + + + + + + To update + https://github.com/qiime2/q2-feature-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (10/11) + (10/11) + (10/11) + (10/11) + False + + + + suite_qiime2__feature_classifier + + + qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global + + + + + + + + + To update + https://github.com/qiime2/q2-feature-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier + 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qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose + + + + + + + + + To update + https://github.com/qiime2/q2-feature-table + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + 2024.2.2+q2galaxy.2024.2.1 + + + (17/22) + (17/22) + (17/22) + (17/22) + False + + + + suite_qiime2__feature_table + + + qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, 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Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table + 2024.2.2+q2galaxy.2024.2.1 + + + (17/22) + (17/22) + (17/22) + (17/22) + False + + + + suite_qiime2__fragment_insertion + + + qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp + + + + + + + + + To update + https://github.com/qiime2/q2-fragment-insertion + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__fragment_insertion + + + qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp + + + + + + + + + To update + https://github.com/qiime2/q2-fragment-insertion + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + suite_qiime2__fragment_insertion + + + qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp + + + + + + + + + To update + https://github.com/qiime2/q2-fragment-insertion + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion + 2024.2.0+q2galaxy.2024.2.1 + + + (3/3) + (3/3) + (3/3) + (3/3) + False + + + + 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qiime2__longitudinal__volatility + + + + + + + + + To update + https://github.com/qiime2/q2-longitudinal + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + 2024.2.0+q2galaxy.2024.2.1 + + + (11/11) + (11/11) + (11/11) + (11/11) + False + + + + suite_qiime2__longitudinal + + + qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility + + + + + + + + + To update + https://github.com/qiime2/q2-longitudinal + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + 2024.2.0+q2galaxy.2024.2.1 + + + (11/11) + (11/11) + (11/11) + (11/11) + False + + + + suite_qiime2__longitudinal + + + qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility + + + + + + + + + To update + https://github.com/qiime2/q2-longitudinal + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + 2024.2.0+q2galaxy.2024.2.1 + + + (11/11) + (11/11) + (11/11) + (11/11) + False + + + + suite_qiime2__longitudinal + + + qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility + + + + + + + + + To update + https://github.com/qiime2/q2-longitudinal + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal + 2024.2.0+q2galaxy.2024.2.1 + + + (11/11) + (11/11) + (11/11) + (11/11) + 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(3/4) + (3/4) + (3/4) + (3/4) + False + + + + suite_qiime2__metadata + + + qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-metadata + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata + 2024.2.0+q2galaxy.2024.2.1 + + + (3/4) + (3/4) + (3/4) + (3/4) + False + + + + suite_qiime2__metadata + + + qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate + + + + + + + + + To update + https://github.com/qiime2/q2-metadata + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata + 2024.2.0+q2galaxy.2024.2.1 + + + (3/4) + (3/4) + (3/4) + (3/4) + False + + + + suite_qiime2__phylogeny + + + qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds + + + + + + + + + To update + https://github.com/qiime2/q2-phylogeny + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__phylogeny + + + qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds + + + + + + + + + To update + https://github.com/qiime2/q2-phylogeny + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__phylogeny + + + qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds + + + + + + + + + To update + https://github.com/qiime2/q2-phylogeny + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__phylogeny + + + qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds + + + + + + + + + To update + https://github.com/qiime2/q2-phylogeny + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny + 2024.2.0+q2galaxy.2024.2.1 + + + (12/12) + (12/12) + (12/12) + (12/12) + False + + + + suite_qiime2__quality_control + + + qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads + + + + + + + + + To update + https://github.com/qiime2/q2-quality-control + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + 2024.2.0+q2galaxy.2024.2.1 + + + (6/10) + (6/10) + (6/10) + (6/10) + False - nanoplot - 1.41.0 - 1.42.0 - nanoplot - To update + suite_qiime2__quality_control + + + qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads + + + - Plotting tool for long read sequencing data and alignments To update - https://github.com/wdecoster/NanoPlot - Visualization - nanoplot - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ + https://github.com/qiime2/q2-quality-control + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + 2024.2.0+q2galaxy.2024.2.1 + + + (6/10) + (6/10) + (6/10) + (6/10) + False - nanopolishcomp - 0.6.11 - 0.6.12 - nanopolishcomp - To update + suite_qiime2__quality_control + + + qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads + + + - NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update - https://a-slide.github.io/NanopolishComp - Sequence Analysis - nanopolishcomp - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp + https://github.com/qiime2/q2-quality-control + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + 2024.2.0+q2galaxy.2024.2.1 + + + (6/10) + (6/10) + (6/10) + (6/10) + False - ncbi_fcs_gx - 0.5.0 - 0.5.0 - ncbi-fcs-gx - Up-to-date + suite_qiime2__quality_control + + + qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads + + - FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). - Up-to-date - https://github.com/ncbi/fcs-gx - Sequence Analysis - ncbi_fcs_gx - iuc - https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx - - - newick_utils - 1.6+galaxy1 - 1.6 - newick_utils - To update - newick_utilities - Newick Utilities - Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction - Phylogeny, Genomics, Computer science - Perform operations on Newick trees - The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. To update - http://cegg.unige.ch/newick_utils - Visualization, Metagenomics - newick_utils - iuc - https://github.com/tjunier/newick_utils + https://github.com/qiime2/q2-quality-control + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control + 2024.2.0+q2galaxy.2024.2.1 + + + (6/10) + (6/10) + (6/10) + (6/10) + False - nextclade - 2.7.0 - 2.14.0 - nextalign - To update + suite_qiime2__quality_filter + + + qiime2__quality_filter__q_score + + + - Identify differences between your sequences and a reference sequence used by Nextstrain To update - https://github.com/nextstrain/nextclade - Sequence Analysis + https://github.com/qiime2/q2-quality-filter + Metagenomics, Sequence Analysis, Statistics - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + 2024.2.0+q2galaxy.2024.2.1 + + + (1/1) + (1/1) + (1/1) + (1/1) + False - nonpareil - 3.1.1 - 3.4.1 - nonpareil - To update + suite_qiime2__quality_filter + + + qiime2__quality_filter__q_score + + + - Estimate average coverage in metagenomic datasets To update - http://nonpareil.readthedocs.io - Metagenomics - nonpareil - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil + https://github.com/qiime2/q2-quality-filter + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + 2024.2.0+q2galaxy.2024.2.1 + + + (1/1) + (1/1) + (1/1) + (1/1) + False - nugen_nudup - 2.3.3 - 2.3.3 - nudup - Up-to-date + suite_qiime2__quality_filter + qiime2__quality_filter__q_score - Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. - Up-to-date - http://nugentechnologies.github.io/nudup/ - SAM, Metagenomics, Sequence Analysis, Transcriptomics - nugen_nudup - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup - - - orfipy - 0.0.4 - 0.0.4 - orfipy - Up-to-date - orfipy - orfipy - Coding region prediction, Database search, Transcriptome assembly, De-novo assembly - Computer science, RNA-Seq, Transcriptomics, Small molecules - Galaxy wrapper for ORFIPY - A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. - Up-to-date - https://github.com/urmi-21/orfipy - Sequence Analysis - orfipy - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy + + + + + To update + https://github.com/qiime2/q2-quality-filter + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + 2024.2.0+q2galaxy.2024.2.1 + + + (1/1) + (1/1) + (1/1) + (1/1) + False - orthofinder - 2.5.5 - 2.5.5 - orthofinder - Up-to-date - OrthoFinder - OrthoFinder - Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment - Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis - Accurate inference of orthologous gene groups made easy - OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. - Up-to-date - https://github.com/davidemms/OrthoFinder - Phylogenetics, Sequence Analysis - orthofinder - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder + suite_qiime2__quality_filter + + + qiime2__quality_filter__q_score + + + + + + + + + To update + https://github.com/qiime2/q2-quality-filter + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter + 2024.2.0+q2galaxy.2024.2.1 + + + (1/1) + (1/1) + (1/1) + (1/1) + False - pharokka - 1.3.2 + suite_qiime2__rescript + + + qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment + + + - \n pharokka\n - To update - \n pharokka\n - rapid standardised annotation tool for bacteriophage genomes and metagenomes To update - https://github.com/gbouras13/pharokka - Genome annotation - pharokka - iuc - https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka + https://github.com/nbokulich/RESCRIPt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + 2024.2.2+q2galaxy.2024.2.1 + + + (0/25) + (0/25) + (0/25) + (0/25) + False - phyloseq - 1.38.0 - 1.46.0 - bioconductor-phyloseq - To update + suite_qiime2__rescript + + + qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment + + + - Handling and analysis of high-throughput microbiome census data To update - https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html - Metagenomics - phyloseq - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq + https://github.com/nbokulich/RESCRIPt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + 2024.2.2+q2galaxy.2024.2.1 + + + (0/25) + (0/25) + (0/25) + (0/25) + False - phyml - 3.3.20220408 - 3.3.20220408 - phyml - Up-to-date - phyml - PhyML - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - Phylogenetics, Bioinformatics, Phylogenetics - PhyML is a phylogeny software based on the maximum-likelihood principle. - Phylogenetic estimation software using Maximum Likelihood - Up-to-date - http://www.atgc-montpellier.fr/phyml/ - Phylogenetics - phyml - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml + suite_qiime2__rescript + + + qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment + + + + + + + + + To update + https://github.com/nbokulich/RESCRIPt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + 2024.2.2+q2galaxy.2024.2.1 + + + (0/25) + (0/25) + (0/25) + (0/25) + False - picrust - 1.1.1 - 1.1.4 - picrust - To update + suite_qiime2__rescript + + + qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment + + - PICRUSt wrappers - To update - https://picrust.github.io/picrust/ - Metagenomics - picrust - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust - - - picrust2 - 2.5.1 - 2.5.2 - picrust2 - To update - picrust2 - PICRUSt2 - Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis - Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing - PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States - PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. To update - https://github.com/picrust/picrust2/wiki - Metagenomics - picrust2 - iuc - https://github.com/picrust/picrust2 + https://github.com/nbokulich/RESCRIPt + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript + 2024.2.2+q2galaxy.2024.2.1 + + + (0/25) + (0/25) + (0/25) + (0/25) + False - plasflow - 1.1.0 - 1.1.0 - plasflow - Up-to-date + suite_qiime2__sample_classifier + qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize - PlasFlow - Prediction of plasmid sequences in metagenomic contigs. - Up-to-date - https://github.com/smaegol/PlasFlow - Sequence Analysis - plasflow - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow - - - plasmidfinder - 2.1.6 - 2.1.6 - plasmidfinder - Up-to-date - PlasmidFinder - PlasmidFinder - Genome assembly, Scaffolding, Multilocus sequence typing - Whole genome sequencing, Sequence assembly, Mapping, Probes and primers - "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" - PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). - Up-to-date - https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ - Sequence Analysis - plasmidfinder - iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder - - - prokka - 1.14.6 - 1.14.6 - prokka - Up-to-date - prokka - Prokka - Gene prediction, Coding region prediction, Genome annotation - Genomics, Model organisms, Virology - Rapid annotation of prokaryotic genomes - Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. - Up-to-date - http://github.com/tseemann/prokka - Sequence Analysis - prokka - crs4 - https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ - - - proteinortho - 6.3.1 - 6.3.1 - proteinortho - Up-to-date - proteinortho - Proteinortho - Homology-based gene prediction - Phylogeny - Proteinortho is a tool to detect orthologous proteins/genes within different species. - Proteinortho is a tool to detect orthologous genes within different species - Up-to-date - https://gitlab.com/paulklemm_PHD/proteinortho - Proteomics - proteinortho - iuc - https://gitlab.com/paulklemm_PHD/proteinortho + + + To update + https://github.com/qiime2/q2-sample-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (15/15) + (15/15) + (15/15) + (15/15) + False - pycoqc - 2.5.2 - 2.5.2 - pycoqc - Up-to-date + suite_qiime2__sample_classifier + qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize - QC metrics for ONT Basecalling - Up-to-date - https://github.com/tleonardi/pycoQC - Nanopore - pycoqc - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc - - - pygenometracks - 3.8 - 3.8 - pygenometracks - Up-to-date - pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. + To update + https://github.com/qiime2/q2-sample-classifier + Metagenomics, Sequence Analysis, Statistics - Up-to-date - https://github.com/deeptools/pyGenomeTracks - Visualization - pygenometracks - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (15/15) + (15/15) + (15/15) + (15/15) + False - qiime_add_on + suite_qiime2__sample_classifier + + + qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize + + - 1.9.1 - qiime - To update - QIIME to perform microbial community analysis To update - http://www.qiime.org - Metagenomics - qiime - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ + https://github.com/qiime2/q2-sample-classifier + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + 2024.2.0+q2galaxy.2024.2.1 + + + (15/15) + (15/15) + (15/15) + (15/15) + False - qiime_core + suite_qiime2__sample_classifier + + + qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize - 1.9.1 - qiime - To update - QIIME to perform microbial community analysis - To update - http://www.qiime.org - Metagenomics - qiime - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ - - - qualimap - 2.2.2d - 2.3 - qualimap - To update - qualimap - QualiMap - Sequencing quality control - Data quality management - Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. To update - http://qualimap.bioinfo.cipf.es/ - Sequence Analysis, Transcriptomics, SAM - qualimap - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap - - + https://github.com/qiime2/q2-sample-classifier + Metagenomics, Sequence Analysis, Statistics - quast - 5.2.0 - 5.2.0 - quast - Up-to-date - quast - QUAST - Visualisation, Sequence assembly validation - Sequence assembly - Quast (Quality ASsessment Tool) evaluates genome assemblies. - QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. - Up-to-date - http://quast.bioinf.spbau.ru/ - Assembly - quast - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast - - + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier + 2024.2.0+q2galaxy.2024.2.1 - quickmerge - 0.3 - 0.3 - quickmerge - Up-to-date - quickmerge - quickmerge - Genome assembly, Scaffolding, De-novo assembly, Genotyping - Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype - Merge long-read and hybrid assemblies to increase contiguity - Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. - Up-to-date - https://github.com/mahulchak/quickmerge - Assembly - quickmerge - galaxy-australia - https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge + + (15/15) + (15/15) + (15/15) + (15/15) + False - raxml - 8.2.12 - 8.2.13 - raxml - To update - raxml - RAxML - Sequence analysis, Phylogenetic tree analysis - Phylogenetics, Sequence analysis - RAxML - A Maximum Likelihood based phylogenetic inference - A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + suite_qiime2__taxa + + + qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table + + + + + + + + To update - http://www.exelixis-lab.org/web/software/raxml/ - Phylogenetics - raxml - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml + https://github.com/qiime2/q2-taxa + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False - read_it_and_keep - 0.2.2 - 0.3.0 - read-it-and-keep - To update + suite_qiime2__taxa + + + qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table + + + - Rapid decontamination of SARS-CoV-2 sequencing reads To update - https://github.com/GenomePathogenAnalysisService/read-it-and-keep - Sequence Analysis - read_it_and_keep - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep - - + https://github.com/qiime2/q2-taxa + Metagenomics, Sequence Analysis, Statistics - recentrifuge - 1.13.2 - 1.13.2 - recentrifuge - Up-to-date - Recentrifuge - Recentrifuge - Taxonomic classification, Expression analysis, Cross-assembly - Metagenomics, Microbial ecology, Metagenomic sequencing - "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." - Robust comparative analysis and contamination removal for metagenomics. - Up-to-date - https://github.com/khyox/recentrifuge - Metagenomics - recentrifuge - iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge - - + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + 2024.2.0+q2galaxy.2024.2.1 - roary - 3.13.0 - 3.13.0 - roary - Up-to-date - roary - Roary - Genome assembly - DNA, Genomics, Mapping - Roary the pangenome pipeline - A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. - Up-to-date - https://sanger-pathogens.github.io/Roary/ - Sequence Analysis - roary - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary + + (4/4) + (4/4) + (4/4) + (4/4) + False - rseqc - 5.0.1 - 5.0.3 - rseqc - To update - rseqc - RSeQC - Data handling - Sequencing - an RNA-seq quality control package - Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. + suite_qiime2__taxa + + + qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table + + + + + + + + To update - https://code.google.com/p/rseqc/ - Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization - rseqc - nilesh - https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc + https://github.com/qiime2/q2-taxa + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False - sarscov2formatter - 1.0 - 1.0 - sarscov2formatter - Up-to-date + suite_qiime2__taxa + qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table - sarscov2formatter custom script - Up-to-date - https://github.com/nickeener/sarscov2formatter - Sequence Analysis - sarscov2formatter - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter + + + + + + To update + https://github.com/qiime2/q2-taxa + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa + 2024.2.0+q2galaxy.2024.2.1 + + + (4/4) + (4/4) + (4/4) + (4/4) + False - sarscov2summary - 0.1 - 0.5 - sarscov2summary - To update + suite_qiime2__vsearch + + + qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref + + + - sarscov2summary custom script To update - https://github.com/nickeener/sarscov2summary - Sequence Analysis - sarscov2summary - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary + https://github.com/qiime2/q2-vsearch + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + 2024.2.0+q2galaxy.2024.2.1 + + + (8/8) + (8/8) + (8/8) + (7/8) + False - scoary - 1.6.16 - 1.6.16 - scoary - Up-to-date + suite_qiime2__vsearch + + + qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref + - Scoary calculates the assocations between all genes in the accessory genome and the traits. - Up-to-date - https://github.com/AdmiralenOla/Scoary - Metagenomics - scoary - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary - - - semibin - 2.0.2 - 2.0.2 - semibin - Up-to-date - semibin - SemiBin - Sequence assembly, Read binning - Metagenomics, Machine learning, Microbial ecology, Sequence assembly - SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks - Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. - Up-to-date - https://semibin.readthedocs.io/en/latest/ - Metagenomics - semibin - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin - - - seqkit - 2.3.1 - 2.6.1 - seqkit - To update - seqkit - seqkit - DNA transcription, Sequence trimming, DNA translation, Sequence conversion - Database management, Sequence analysis - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. To update - https://bioinf.shenwei.me/seqkit/ - Sequence Analysis - seqkit - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit + https://github.com/qiime2/q2-vsearch + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + 2024.2.0+q2galaxy.2024.2.1 + + + (8/8) + (8/8) + (8/8) + (7/8) + False - seqsero2 - 1.2.1 - 1.2.1 - seqsero2 - Up-to-date + suite_qiime2__vsearch + qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref - Salmonella serotype prediction from genome sequencing data - Up-to-date - https://github.com/denglab/SeqSero2 - Sequence Analysis - seqsero2 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 - - - shovill - 1.1.0 - 1.1.0 - shovill - Up-to-date - shovill - shovill - Genome assembly - Genomics, Microbiology, Sequence assembly - Faster de novo assembly pipeline based around Spades - Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. - Up-to-date - https://github.com/tseemann/shovill - Assembly - shovill - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill - - - smallgenomeutilities - 0.4.0 - 0.4.0 - smallgenomeutilities - Up-to-date - v-pipe - V-pipe - Read pre-processing, Sequence alignment, Genetic variation analysis - Genomics, Population genetics, Workflows, Virology, Sequencing - Set of utilities for manipulating small viral genome data. - Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. - Up-to-date - https://github.com/cbg-ethz/smallgenomeutilities - Sequence Analysis - smallgenomeutilities - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities - - - snap - 2013_11_29 - 2013_11_29 - snap - Up-to-date - snap - SNAP - Gene prediction - DNA, DNA polymorphism, Genetics - SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. - The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. - Up-to-date - https://github.com/KorfLab/SNAP - Sequence Analysis - snap - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap - - - snippy - 4.6.0 - snippy - To update - snippy - snippy - Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling - Genomics, Model organisms, DNA polymorphism, Phylogenetics - Contains the snippy tool for characterising microbial snps - Rapid haploid variant calling and core SNP phylogeny generation. To update - https://github.com/tseemann/snippy - Sequence Analysis - snippy - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy + https://github.com/qiime2/q2-vsearch + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + 2024.2.0+q2galaxy.2024.2.1 + + + (8/8) + (8/8) + (8/8) + (7/8) + False - sonneityping - 20210201 - 20210201 - sonneityping - Up-to-date + suite_qiime2__vsearch + qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref - Scripts for parsing Mykrobe predict results for Shigella sonnei. - Up-to-date - https://github.com/katholt/sonneityping - Sequence Analysis - sonneityping - iuc - https://github.com/katholt/sonneityping - - - spades - 3.15.5 - 3.15.5 - spades - Up-to-date - SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. + To update + https://github.com/qiime2/q2-vsearch + Metagenomics, Sequence Analysis, Statistics - Up-to-date - https://github.com/ablab/spades - Assembly, RNA, Metagenomics - spades - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades - - + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch + 2024.2.0+q2galaxy.2024.2.1 - spotyping - 2.1 - 2.1 - spotyping - Up-to-date - spotyping - SpoTyping - Variant pattern analysis - Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation - SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads - Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. - Up-to-date - https://github.com/xiaeryu/SpoTyping-v2.0 - Sequence Analysis - spotyping - iuc - https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine + + (8/8) + (8/8) + (8/8) + (7/8) + False - srst2 - 0.2.0 - 1.19.2 - samtools - To update + suite_qiime2_core + + - SRST2 Short Read Sequence Typing for Bacterial Pathogens - To update - http://katholt.github.io/srst2/ - Metagenomics - srst2 - iuc - https://github.com/katholt/srst2 - - - structure - 2.3.4 - 2.3.4 - structure - Up-to-date - structure - Structure - Genetic variation analysis - Population genetics - for using multi-locus genotype data to investigate population structure. - The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. - Up-to-date - Phylogenetics, Variant Analysis - structure - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure - - - taxonomy_krona_chart - 2.7.1+galaxy0 - 2.8.1 - krona - To update - krona - Krona - Visualisation - Metagenomics - Krona pie chart from taxonomic profile - Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). - To update - http://sourceforge.net/projects/krona/ - Assembly - taxonomy_krona_chart - crs4 - https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart - - - tb-profiler - 4.4.1 - 5.0.1 - tb-profiler To update + Statistics, Metagenomics, Sequence Analysis + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core - Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. - To update - https://github.com/jodyphelan/TBProfiler - Sequence Analysis - tbprofiler - iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler + + (0/1) + (0/1) + (0/1) + (0/1) + False - transtermhp + suite_qiime2_core + + - 2.09 - transtermhp - To update - Finds rho-independent transcription terminators in bacterial genomes - To update - Sequence Analysis - transtermhp - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp - - - unicycler - 0.5.0 - 0.5.0 - unicycler - Up-to-date - unicycler - Unicycler - Genome assembly, Aggregation - Microbiology, Genomics, Sequencing, Sequence assembly - Unicycler is a hybrid assembly pipeline for bacterial genomes. - A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. - Up-to-date - https://github.com/rrwick/Unicycler - Assembly - unicycler - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler - - - usher - 0.2.1 - 0.6.3 - usher To update + Statistics, Metagenomics, Sequence Analysis + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core - UShER toolkit wrappers - To update - https://github.com/yatisht/usher - Phylogenetics - usher - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher + + (0/1) + (0/1) + (0/1) + (0/1) + False - valet + suite_qiime2_core + + + + + - 1.0 - valet - To update - A pipeline for detecting mis-assemblies in metagenomic assemblies. To update - https://github.com/marbl/VALET - Metagenomics - valet - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet - - - vapor - 1.0.2 - 1.0.2 - vapor - Up-to-date - vapor - VAPOR - Data retrieval, De-novo assembly, Read mapping - Whole genome sequencing, Mapping, Sequence assembly - Classify Influenza samples from raw short read sequence data - VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. - Up-to-date - https://github.com/connor-lab/vapor - Sequence Analysis - vapor - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor - - + Statistics, Metagenomics, Sequence Analysis - varvamp - 1.1.1 - 1.1.1 - varvamp - Up-to-date - varvamp - varVAMP - PCR primer design - Virology - Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses - variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. - Up-to-date - https://github.com/jonas-fuchs/varVAMP/ - Sequence Analysis - varvamp - iuc - https://github.com/jonas-fuchs/varVAMP + q2d2 + + https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core + + + + (0/1) + (0/1) + (0/1) + (0/1) + False - vegan - 2.4-3 - 2.3_4 - r-vegan - To update + suite_qiime2_core + - To update - https://cran.r-project.org/package=vegan - Metagenomics - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ - - - velvet - 1.2.10 - velvet - To update - velvet - Velvet - Formatting, De-novo assembly - Sequence assembly - de novo genomic assembler specially designed for short read sequencing technologies - A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. - To update - https://www.ebi.ac.uk/~zerbino/velvet/ - Assembly - velvet - devteam - https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet - - - velvet_optimiser - 2.2.6+galaxy2 - 1.2.10 - velvet - To update - velvetoptimiser - VelvetOptimiser - Optimisation and refinement, Sequence assembly - Genomics, Sequence assembly - Automatically optimize Velvet assemblies - This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. To update - Assembly - velvetoptimiser - simon-gladman - https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser + Statistics, Metagenomics, Sequence Analysis + + q2d2 + + https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core + + + + (0/1) + (0/1) + (0/1) + (0/1) + False - vsearch - 2.8.3 - 2.27.0 - vsearch - To update - vsearch - VSEARCH - DNA mapping, Chimera detection - Metagenomics, Sequence analysis - VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. - High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + suite_qiime2_core__tools + + + qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq + + + + + + + + To update - https://github.com/torognes/vsearch - Sequence Analysis - vsearch - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch + https://qiime2.org + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + 2024.2.1+dist.he188c3c2 + + + (2/3) + (2/3) + (2/3) + (2/3) + False - windowmasker - 1.0 - 2.15.0 - blast - To update + suite_qiime2_core__tools + + + qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq + + + - Identify repetitive regions using WindowMasker To update - https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ - Sequence Analysis - windowmasker - iuc - https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ + https://qiime2.org + Metagenomics, Sequence Analysis, Statistics + + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + 2024.2.1+dist.he188c3c2 + + + (2/3) + (2/3) + (2/3) + (2/3) + False - bamtools - 2.5.2 - 2.5.2 - bamtools - Up-to-date + suite_qiime2_core__tools + qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq - Operate on and transform BAM datasets in various ways using bamtools - Up-to-date - https://github.com/pezmaster31/bamtools - Sequence Analysis, SAM - bamtools - devteam - https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools - - - biotradis - 1.4.5 - 1.4.5 - biotradis - Up-to-date - Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. + To update + https://qiime2.org + Metagenomics, Sequence Analysis, Statistics - Up-to-date - https://www.sanger.ac.uk/science/tools/bio-tradis - Genome annotation - biotradis - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + 2024.2.1+dist.he188c3c2 + + + (2/3) + (2/3) + (2/3) + (2/3) + False - kraken + suite_qiime2_core__tools + + + qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq + + + + + + + - 1.1.1 - kraken To update + https://qiime2.org + Metagenomics, Sequence Analysis, Statistics + q2d2 + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools + 2024.2.1+dist.he188c3c2 + (2/3) + (2/3) + (2/3) + (2/3) + False + + - Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. + t2ps + 457.0 + 31.0 + Draw_phylogram + Draw phylogeny + t2ps + t2ps + Draw phylogeny + "Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper + Phylogenetic tree visualisation + Phylogenomics To update - http://ccb.jhu.edu/software/kraken/ + https://bitbucket.org/natefoo/taxonomy Metagenomics - kraken + t2ps devteam - https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps + 1.0.0 + taxonomy + 0.10.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - kraken2 - 2.1.1 - 2.1.3 - kraken2 - To update + t2t_report + 947.0 + 26.0 + t2t_report + Summarize taxonomy + + - Kraken2 for taxonomic designation. To update - http://ccb.jhu.edu/software/kraken/ + https://bitbucket.org/natefoo/taxonomy Metagenomics - kraken2 - iuc - https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ + t2t_report + devteam + https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report + https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report + 1.0.0 + taxonomy + 0.10.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - eggnog_mapper - 2.1.8 - 2.1.12 - eggnog-mapper - To update - eggnog-mapper-v2 - eggNOG-mapper v2 - Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval - Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis - eggnog-mapper fast functional annotation of novel sequences - EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. - To update + t_coffee + 8690.0 + 70.0 + t_coffee + T-Coffee - Proteomics - eggnog_mapper - galaxyp - https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper - - - metagene_annotator - 1.0.0 - 1.0 - metagene_annotator - To update - MetaGeneAnnotator gene-finding program for prokaryote and phage To update - + http://www.tcoffee.org/ Sequence Analysis - metagene_annotator - galaxyp - https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator + t_coffee + earlhaminst + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee + https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee + 13.45.0.4846264 + t-coffee + 13.46.0.919e8c6b + (0/1) + (0/1) + (1/1) + (0/1) + False - Geom_mean_workflow - 0.1.0+galaxy0 + taxonomy_krona_chart + 27426.0 + 1801.0 + taxonomy_krona_chart + Krona pie chart from taxonomic profile + krona + krona - r-base + Krona + Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). + Visualisation + Metagenomics To update + http://sourceforge.net/projects/krona/ + Assembly + taxonomy_krona_chart + crs4 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart + https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart + 2.7.1+galaxy0 + krona + 2.8.1 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + tb-profiler + tb_profiler_profile + Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. + tb-profiler + tb-profiler - Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). + tb-profiler + A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). + Antimicrobial resistance prediction - To update - https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom - Ecology - Geometric means (Dead wood) - ecology - https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow + Up-to-date + https://github.com/jodyphelan/TBProfiler + Sequence Analysis + tbprofiler + iuc + https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler + https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler + 6.2.1 + tb-profiler + 6.2.1 + (1/1) + (1/1) + (1/1) + (0/1) + False - PAMPA - 0.0.2 + tooldistillator - To update + tooldistillator, tooldistillator_summarize + ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files + tooldistillator + tooldistillator + ToolDistillator + ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. + Data handling, Parsing + Microbiology, Bioinformatics, Sequence analysis + Up-to-date + https://gitlab.com/ifb-elixirfr/abromics/tooldistillator + Sequence Analysis + tooldistillator + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator + https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator + 0.8.5.0 + tooldistillator + 0.8.5.0 + (0/2) + (0/2) + (2/2) + (2/2) + False + + + transit - Tools to compute and analyse biodiversity metrics + gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps + TRANSIT + transit + transit + TRANSIT + A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. + Transposon prediction + DNA, Sequencing, Mobile genetic elements To update + https://github.com/mad-lab/transit/ + Genome annotation - Ecology - pampa - ecology - https://github.com/ColineRoyaux/PAMPA-Galaxy + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit + 3.0.2 + transit + 3.2.3 + (5/5) + (5/5) + (5/5) + (0/5) + False - interpolation - 1.0 + transtermhp + 229.0 + 5.0 + transtermhp + Finds rho-independent transcription terminators in bacterial genomes + transtermhp + transtermhp + + TransTermHP + TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator + Transcriptional regulatory element prediction + Transcription factors and regulatory sites + To update + https://transterm.cbcb.umd.edu + Sequence Analysis + transtermhp + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp + https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp + + transtermhp + 2.09 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + + trim_galore + 238699.0 + 2334.0 + trim_galore + Trim Galore adaptive quality and adapter trimmer + trim_galore + trim_galore - r-getopt + Trim Galore + A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + Sequence trimming, Primer removal, Read pre-processing + Sequence analysis To update + http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ + Sequence Analysis, Fastq Manipulation + trim_galore + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore + https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore + 0.6.7 + trim-galore + 0.6.10 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + trycycler + + + trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample + Trycycler toolkit wrappers + + + - Run IDW interpolation based on a .csv and .geojson file + Up-to-date + https://github.com/rrwick/Trycycler + Assembly + trycycler + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler + https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler + 0.5.5 + trycycler + 0.5.5 + (0/5) + (5/5) + (5/5) + (5/5) + False + + + + unicycler + 65732.0 + 1558.0 + unicycler + Unicycler is a hybrid assembly pipeline for bacterial genomes. + unicycler + unicycler + + Unicycler + A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. + Genome assembly, Aggregation + Microbiology, Genomics, Sequencing, Sequence assembly + Up-to-date + https://github.com/rrwick/Unicycler + Assembly + unicycler + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler + https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler + 0.5.0 + unicycler + 0.5.0 + (1/1) + (1/1) + (1/1) + (1/1) + False + + + + unipept + 5005.0 + 115.0 + unipept + Unipept retrieves metaproteomics information + unipept + unipept + Unipept + Metaproteomics data analysis with a focus on interactive data visualizations. + Prediction and recognition, Visualisation + Proteomics, Proteogenomics, Biodiversity, Workflows To update - https://github.com/AquaINFRA/galaxy - Ecology + https://github.com/galaxyproteomics/tools-galaxyp + Proteomics + unipept + galaxyp + https://unipept.ugent.be/apidocs + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept + 4.5.1 + python - ecology - https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation + (1/1) + (1/1) + (1/1) + (0/1) + False - obisindicators - 0.0.2 + uniprotxml_downloader + 1360.0 + 79.0 + uniprotxml_downloader + Download UniProt proteome in XML or fasta format + - r-base - To update - Compute biodiveristy indicators for marine data from obis To update - https://github.com/Marie59/obisindicators - Ecology - ecology - https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators + Proteomics + uniprotxml_downloader + galaxyp + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader + https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader + 2.4.0 + requests + + (0/1) + (1/1) + (1/1) + (0/1) + False - ocean - 0.1.15 - + usher + 1060.0 + 5.0 + usher_matutils, usher + UShER toolkit wrappers + usher + usher + usher + The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. + Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) + Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update + https://github.com/yatisht/usher + Phylogenetics + usher + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher + https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher + 0.2.1 + usher + 0.6.3 + (0/2) + (0/2) + (2/2) + (0/2) + False + + + valet + 637.0 + 20.0 + valet + A pipeline for detecting mis-assemblies in metagenomic assemblies. + valet + valet - - - Access, process, visualise oceanographic data for the Earth System - + VALET + VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. + Sequence assembly, Sequence assembly visualisation + Metagenomics, Sequence assembly To update - https://github.com/Marie59/FE-ft-ESG/tree/main/argo - Ecology + https://github.com/marbl/VALET + Metagenomics + valet + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet + https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet - ecology - https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean + valet + 1.0 + (1/1) + (0/1) + (1/1) + (1/1) + False - blast2go - 0.0.11 - - b2g4pipe - To update + vapor + 3164.0 + 94.0 + vapor + Classify Influenza samples from raw short read sequence data + vapor + vapor + VAPOR + VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. + Data retrieval, De-novo assembly, Read mapping + Whole genome sequencing, Mapping, Sequence assembly + Up-to-date + https://github.com/connor-lab/vapor + Sequence Analysis + vapor + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor + https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor + 1.0.2 + vapor + 1.0.2 + (1/1) + (0/1) + (1/1) + (0/1) + False + + + varvamp - Maps BLAST results to GO annotation terms + varvamp + Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses + varvamp + varvamp - To update - https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go - Ontology Manipulation, Sequence Analysis - blast2go - peterjc - https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go + varVAMP + variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. + PCR primer design + Virology + Up-to-date + https://github.com/jonas-fuchs/varVAMP/ + Sequence Analysis + varvamp + iuc + https://github.com/jonas-fuchs/varVAMP + https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp + 1.2.0 + varvamp + 1.2.0 + (0/1) + (0/1) + (1/1) + (0/1) + False - blast_rbh - 0.3.0 - 1.70 - biopython - To update - - + vegan - BLAST Reciprocal Best Hits (RBH) from two FASTA files + vegan_diversity, vegan_fisher_alpha, vegan_rarefaction + an R package fo community ecologist + vegan + vegan + vegan + Ordination methods, diversity analysis and other functions for community and vegetation ecologists + Standardisation and normalisation, Analysis + Ecology, Phylogenetics, Environmental science To update - https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh - Fasta Manipulation, Sequence Analysis - blast_rbh - peterjc - https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh + https://cran.r-project.org/package=vegan + Metagenomics + + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan + 2.4-3 + r-vegan + 2.3_4 + (3/3) + (0/3) + (3/3) + (0/3) + False - blastxml_to_top_descr - 0.1.2 + velvet + 12218.0 + 1280.0 + velvetg, velveth + de novo genomic assembler specially designed for short read sequencing technologies + velvet + velvet - python + Velvet + A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. + Formatting, De-novo assembly + Sequence assembly To update + https://www.ebi.ac.uk/~zerbino/velvet/ + Assembly + velvet + devteam + https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet + https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet + velvet + 1.2.10 + (2/2) + (2/2) + (2/2) + (2/2) + False + + + velvet_optimiser - Make table of top BLAST match descriptions + velvetoptimiser + Automatically optimize Velvet assemblies + velvetoptimiser + velvetoptimiser + VelvetOptimiser + This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. + Optimisation and refinement, Sequence assembly + Genomics, Sequence assembly To update - https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr - Convert Formats, Sequence Analysis, Text Manipulation - blastxml_to_top_descr - peterjc - https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr + + Assembly + velvetoptimiser + simon-gladman + https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser + https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser + 2.2.6+galaxy2 + velvet + 1.2.10 + (1/1) + (1/1) + (1/1) + (0/1) + False - make_nr - 0.0.2 - 1.70 - biopython - To update - + virAnnot + virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv + virAnnot wrappers + virannot + virannot - Make a FASTA file non-redundant - + virAnnot + VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. + Sequence annotation, Sequence clustering, Sequence cluster visualisation + Metagenomics, Virology, Microbial ecology To update - https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr - Fasta Manipulation, Sequence Analysis - make_nr - peterjc - https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr + https://github.com/marieBvr/virAnnot + Metagenomics + virannot + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot + https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot + 1.0.0+galaxy0 + biopython + 1.70 + (0/3) + (0/3) + (3/3) + (3/3) + False - ncbi_blast_plus - 2.14.1 + vsearch + 8507.0 + 182.0 + vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting + VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. + vsearch + vsearch - python + VSEARCH + High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + DNA mapping, Chimera detection + Metagenomics, Sequence analysis To update + https://github.com/torognes/vsearch + Sequence Analysis + vsearch + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch + https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch + 2.8.3 + vsearch + 2.28.1 + (8/8) + (8/8) + (8/8) + (8/8) + False + + + wtdbg + 1660.0 + 116.0 + wtdbg + WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. + wtdbg2 + wtdbg2 - - - NCBI BLAST+ - - To update - https://blast.ncbi.nlm.nih.gov/ - Sequence Analysis - ncbi_blast_plus - devteam - https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus + wtdbg2 + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. + Genome assembly, De-novo assembly + Sequence assembly, Sequencing + Up-to-date + https://github.com/ruanjue/wtdbg2 + Assembly + wtdbg + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg + https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg + 2.5 + wtdbg + 2.5 + (0/1) + (0/1) + (1/1) + (1/1) + False diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv index fcbcc977..f6e69616 100644 --- a/results/microgalaxy/tools.tsv +++ b/results/microgalaxy/tools.tsv @@ -1,748 +1,364 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu Reviewed To keep -braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) True False -braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.6 (0/1) (1/1) (1/1) True False -helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 (0/1) (0/1) (1/1) True False -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) True False -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest 2.0 (0/4) (0/4) (0/4) True False -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ 0.3.1 (0/1) (0/1) (1/1) True False -TreeBest treebest_best TreeBeST best To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) True True -blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) True False -ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) True True -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) True False -hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) True False -hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) True False -lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) True True -miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) True False -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True False -t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) True False -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) True True -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True True -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl (0/1) (0/1) (0/1) True False -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) True False -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) True True -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) True False -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml 5.1.0 gawk (1/1) (1/1) (1/1) True False -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml 0.1 (0/1) (0/1) (0/1) True False -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) True True -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml 0.1 (0/1) (0/1) (0/1) True False -cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) True True -ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) True True -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True False -fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True False -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True False -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) True False -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True True -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) True True -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) True True -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml 0.3.0 kaptive 2.0.6 (0/1) (0/1) (0/1) True False -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml 2.3 kat 2.4.2 (0/1) (0/1) (0/1) True True -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) True False -mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) True True -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) True True -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base (0/1) (0/1) (0/1) True True -pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) True False -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist 0.1.2 python (0/1) (0/1) (0/1) True False -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml (0/1) (0/1) (0/1) True False -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml 1.1 spades 3.15.5 (0/1) (0/1) (0/1) True True -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer 1.2 python (0/1) (0/1) (0/1) True True -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) True False -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) True False -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) True False -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) True False -sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml 1.1.1 sistr_cmd 1.1.1 (0/1) (1/1) (1/1) True True -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) True True -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) True False -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml 1.0.1 spolpred (0/1) (0/1) (0/1) True False -srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) True True -staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) True True -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) True True -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) True False -isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) True False -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) False -best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) True False -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) True False -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) True False -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) True True -compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) True False -compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) True False -count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) True False -ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) True False -cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) True False -delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) True False -divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) True False -express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) True False -featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter 2.0.0 bx-python 0.10.0 (1/1) (0/1) (1/1) True False -filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) True False -generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) True False -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) True False -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) True False -gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) True False -hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) True False -indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) True False -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) True False -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) True False -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) True False -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) True False -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) True False -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability 1.1.0 bx-python 0.10.0 (1/1) (0/1) (0/1) True False -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) True True -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 1.0.1 bx-python 0.10.0 (0/1) (0/1) (0/1) True True -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) True False -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) True False -short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) True False -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) True False -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) True False -tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat 1.5.0 samtools 1.19.2 (0/1) (0/1) (0/1) True False -tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 2.1.1 bowtie2 2.5.3 (1/1) (1/1) (1/1) True False -ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) True False -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) True False -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) True False -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) True False -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) True False -find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True False -gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk (1/1) (1/1) (1/1) True True -lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 (0/1) (1/1) (1/1) True False -t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) True False -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) True False -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False -antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 (1/1) (1/1) (1/1) True True -augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) True False -bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) True False -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.0 (0/1) (0/1) (0/1) True False -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) True False -bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (0/4) (4/4) True False -blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) True False -blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) True False -chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) True False -circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) True False -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann Combine Metaphlan and HUMAnN """This tool combine MetaPhlAn outputs and HUMANnN outputs."" - Galaxy tool wrapper" Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 0.3.0 python (0/1) (0/1) (1/1) True True -compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs Compare HUMAnN2 outputs """This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples."" - Galaxy tool wrapper" Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) True True -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) True False -flye 20904.0 1499.0 flye Assembly of long and error-prone reads. To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.1 flye 2.9.3 (1/1) (1/1) (1/1) True True -format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output Format metaphlan2 output """This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)."" - Galaxy tool wrapper" Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 (0/1) (0/1) (1/1) True True -gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) True False -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) True True -gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) True False -graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) True False -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) True True -hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler Up-to-date https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.8 (1/1) (1/1) (1/1) True False -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) True False -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) True False -instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) True False -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) True True -itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) True True -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) True False -lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data To update Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/mourisl/Lighter 1.0 lighter 1.1.2 (0/1) (0/1) (1/1) True True -mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.508 mafft 7.520 (2/2) (2/2) (2/2) True True -mcl 29.0 10.0 mcl_clustering Markov Cluster Algorithm To update http://micans.org/mcl/ Sequence Analysis, Metagenomics mcl bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mcl 14.137 mcl 22.282 (0/1) (0/1) (0/1) True True -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) True False -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) True False -metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) True False -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) True False -minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) True False -minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) True True -mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (0/1) (1/1) True False -nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) True True -nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) True True -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (0/140) (34/140) (135/140) True False -peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) True False -pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) True True -piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) True False -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) True False -plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas (1/1) (1/1) (1/1) True False -plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) True False -plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) True False -protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) True False -protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) True False -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) True False -racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads Genome assembly, Mapping assembly, Sequence trimming Whole genome sequencing, Sequence assembly, Plant biology Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) True True -repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) True False -antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) True False -aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) True False -blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) True False -cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy0 perl (0/1) (0/1) (1/1) True False -cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) True False -cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) True False -compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ 1.0 compalignp 1.0 (0/1) (0/1) (1/1) True False -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) True False -dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) True False -dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 (0/1) (0/1) (1/1) True False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 (0/1) (0/1) (0/1) True False -dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) True False -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) True False -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) True False -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) True False -infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs Up-to-date http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal 1.1.4 infernal 1.1.4 (0/6) (6/6) (6/6) True True -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) True False -intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) True False -kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) True False -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) True False -mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) True False -mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 (0/1) (0/1) (1/1) True False -nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) True False -paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) True False -pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) True False -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) True True -rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) False -rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) True False -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (0/1) True True -remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) True False -ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) True False -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) True False -rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) True False -rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) True False -rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) True False -rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) True False -rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) True False -rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) True False -selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) True False -sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) True True -sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) True False -targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) True False -trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) True False -vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) True False -sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) True False -salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.2 (2/3) (1/3) (3/3) True True -tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) True False -trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) True True -uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.4 requests (1/1) (1/1) (1/1) True False -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) True False -wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) True True -align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) True False -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) True False -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.19.2 (0/2) (0/2) (0/2) True False -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) True True -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.19.2 (0/1) (0/1) (0/1) True False -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.19.2 (0/1) (0/1) (0/1) True False -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.20 effectiveT3 1.0.1 (0/1) (0/1) (0/1) True True -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) True False -mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) True False -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) True False -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) True False -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) True False -sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) True False -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.19.2 (0/1) (0/1) (0/1) True False -samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.19.2 (1/1) (0/1) (1/1) True False -samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.19.2 (1/1) (1/1) (1/1) True False -seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) True False -seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) True False -seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) True False -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) True False -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) True False -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) True False -venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) True False -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) True False -abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) True True -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr 1.0.14 abritamr 1.0.14 (0/1) (0/1) (0/1) True True -abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly To update http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss 2.3.6 abyss 2.3.7 (0/1) (1/1) (1/1) True True -adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) True False -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) True False -aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) True True -amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) True True -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 2.7.22 (0/19) (0/19) (19/19) True False -amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.11.26 (0/1) (0/1) (1/1) True True -ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) True True -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.10.3 anndata 0.6.22.post1 (5/5) (3/5) (5/5) True False -annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.17.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) True False -arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) True False -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (0/3) True False -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) True True -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) True False -augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) True False -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) True False -bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.9.2 (0/1) (1/1) (1/1) True True -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) True False -bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) True True -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 (4/4) (0/4) (4/4) True False -barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) True False -bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) True False -bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) True True -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.01 bbmap 39.01 (1/6) (1/6) (5/6) True False -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) True False -bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) True False -binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) True True -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python (1/1) (0/1) (1/1) True False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) True True -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) True False -biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) True False -blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) True False -bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken 2.9 bracken 2.9 (0/1) (0/1) (1/1) True True -busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.6.1 (1/1) (1/1) (1/1) True True -bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) True False -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) True False -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) True True -cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) True True -cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) True True -charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt (0/1) (0/1) (0/1) True False -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) True True -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) True False -chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) True False -chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) True False -circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) True False -clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 0.1.12 clair3 1.0.5 (0/1) (0/1) (1/1) True False -clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins " - clustal2 - " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) True True -codeml 60901.0 29.0 codeml Detects positive selection To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) True True -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) True True -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) True False -concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) True True -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) True False -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics To update https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm 0.6.1 coverm 0.7.0 (0/2) (0/2) (2/2) True True -crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) True False -crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) True False -cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt 4.6 cutadapt 4.6 (1/1) (1/1) (1/1) True True -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) True True -das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics To update https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool 1.1.6 das_tool 1.1.7 (0/2) (0/2) (2/2) True True -deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) True False -deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis Transcriptomics To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) True False -dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) True False -diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond 2.0.15 diamond 2.1.8 (3/3) (3/3) (3/3) True True -disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ disco 1.2 (1/1) (0/1) (1/1) True True -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) True True -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.4.5 (0/2) (0/2) (2/2) True True -dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) True False -edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) True False -egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) True False -emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) True False -exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) True False -exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) True False -export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) True True -fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) True True -fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) True False -fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy (1/1) (1/1) (1/1) True False -fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc 1.3 fastani 1.34 (0/1) (0/1) (1/1) True False -fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files " - fastp - " To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1) True True -fastqe 4333.0 1266.0 fastqe FASTQE To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) True True -fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) True True -featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation Sequencing To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) True False -feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) True False -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) True False -fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) True False -filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality " - filtlong - " Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) True True -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) True False -flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) True False -fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ fraggenescan 1.31 (0/1) (1/1) (1/1) True True -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.8 (2/4) (0/4) (4/4) True True -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " - funannotate - " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) True True -gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) True False -gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) True False -geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) True False -genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) True False -getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle 1.7.7.0 getorganelle 1.7.7.0 (0/2) (2/2) (2/2) True False -gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) True False -gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) True False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base (5/5) (2/5) (5/5) True False -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) True True -goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) True True -goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) True True -graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees To update https://bitbucket.org/nsegata/graphlan/overview Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ graphlan 1.1.3 (2/2) (2/2) (2/2) True True -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) True True -gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.1 (1/1) (1/1) (1/1) True True -gwastools gwastools_manhattan_plot gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) True False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 (0/2) (0/2) (2/2) True True -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) True True -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) True False -hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog 1.3.6 hapog 1.3.7 (0/1) (0/1) (1/1) True False -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 3.1.3 r-gplots 2.17.0 (1/1) (1/1) (1/1) True False -heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. bionet BioNet This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) True False -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) True False -hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff 3.1.5 hicstuff 3.2.1 (0/1) (0/1) (0/1) True False -hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) True True -hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) True False -hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families To update http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 3.3.2 hmmer 3.4 (0/12) (12/12) (12/12) True True -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) True False -htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis To update https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count 0.9.1+galaxy1 htseq 2.0.5 (1/1) (1/1) (1/1) True False -humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (6/13) (13/13) True True -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper 2.1.6 hybpiper 2.1.6 (0/1) (1/1) (0/1) True False -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ 2.5.47 hyphy 2.5.59 (17/17) (2/17) (17/17) True True -hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) True True -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.1 icescreen 1.3.1 (0/1) (0/1) (0/1) True True -idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) True True -idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) True False -iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) True False -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain 1.5.3 instrain 1.8.0 (0/2) (0/2) (2/2) True True -integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis To update https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder 2.0.2 hmmer 3.4 (0/1) (1/1) (1/1) True False -interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) True True -iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood To update http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ 2.1.2 iqtree 2.2.6 (1/1) (1/1) (1/1) True True -isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) True False -isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) True False -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) True True -jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) True True -jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) True False -jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.0 (0/1) (1/1) (1/1) True True -kc-align kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) True True -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) True True -kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) True True -kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) True True -kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) True True -kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (0/1) (1/1) True True -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 (1/6) (2/6) (6/6) True True -krocus krocus Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (0/1) True True -last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last 1205 last 1526 (0/5) (0/5) (5/5) True False -legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) True True -length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) True False -limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics To update http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom 3.50.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) True False -lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot 1.4.0 r-base (0/1) (0/1) (1/1) True True -links 405.0 77.0 links Scaffold genome assemblies with long reads. links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) True False -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) True True -m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) True True -maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 0.99.12 maaslin2 0.99.12 (0/1) (0/1) (1/1) True True -macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) True False -maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) True True -mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) True True -mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) True True -masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) True False -maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ maxbin2 2.2.7 (1/1) (1/1) (1/1) True True -mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) True True -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) True True -megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) True True -megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) True True -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.24.20 (0/7) (0/7) (7/7) True True -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) True True -merqury 2483.0 244.0 merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True -meryl 6785.0 350.0 meryl Meryl a k-mer counter. meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True -metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ 2.15 metabat2 2.15 (1/2) (1/2) (2/2) True True -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) True True -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) True True -metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ 4.0.6 metaphlan 4.0.6 (1/4) (2/4) (4/4) True True -migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) True False -minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) True True -miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) True True -miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot 0.12 miniprot 0.12 (0/2) (0/2) (2/2) True True -mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 (0/1) (0/1) (1/1) True False -mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) True False -mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos 1.1.5 mitos 2.1.7 (1/2) (1/2) (2/2) True True -mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Taxonomic classification Immunoproteins, genes and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) True True -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) True True -multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules To update https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea 1.8.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) True True -multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation Sequencing, Bioinformatics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc 1.11 multiqc 1.19 (1/1) (1/1) (1/1) True True -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mumer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) True False -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) True True -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) True False -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) True True -nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments To update https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ 1.41.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) True True -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) True True -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (0/1) False -necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) True False -newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) True True -nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) True True -nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) True True -novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty 4.3.1 novoplasty 4.3.3 (0/1) (1/1) (1/1) True False -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) True True -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) True False -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.4 (0/2) (0/2) (2/2) True False -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.2 (0/4) (0/4) (4/4) True False -optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) True False -orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) True True -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) True True -pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) True False -parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) True False -pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) True False -pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr Reviewed Deprecated To keep +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 (0/5) (5/5) (5/5) (5/5) True False True +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) (0/1) True False True +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) (1/1) True False True +abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) True False True +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) True False True +abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.7 abyss 2.3.7 (0/1) (1/1) (1/1) (0/1) True False True +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) (0/1) True False True +amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) (0/1) True False True +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) (1/1) True False True +ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) (0/1) True False True +antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 (1/1) (1/1) (1/1) (0/1) True False True +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) (0/2) True False True +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False True +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.3 bakta 1.9.3 (0/1) (1/1) (1/1) (1/1) True False True +bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) True False True +bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) (2/2) True False True +bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) (0/1) True False True +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) (0/6) True False True +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 (0/1) (0/1) (1/1) (0/1) True False True +binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) (0/1) True False True +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) (0/1) True False True +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (6/6) (0/6) True False True +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) True False True +blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) (0/1) True False True +blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False True +blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) (0/1) True False True +bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (1/1) (1/1) (1/1) (1/1) True False True +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) True False True +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) True False True +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) (0/1) True False True +cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) True False True +cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) (0/1) True False True +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) (10/10) True False True +clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 0.1.12 clair3 1.0.8 (0/1) (0/1) (1/1) (0/1) True False True +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) (0/1) True False True +clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) True False True +cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl (0/1) (0/1) (1/1) (0/1) True False True +codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) True False True +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) True False True +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) (0/1) True False True +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python (0/1) (0/1) (1/1) (0/1) True False True +compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) (0/1) True False True +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) True False True +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) True False True +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) True False True +cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) (0/1) True False True +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.8 cutadapt 4.8 (1/1) (1/1) (1/1) (1/1) True False True +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) True False True +das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 (0/2) (0/2) (2/2) (2/2) True False True +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) True False True +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) True False True +disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 (1/1) (0/1) (1/1) (0/1) True False True +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.3.5 dram 1.5.0 (0/5) (0/5) (5/5) (0/5) True False True +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 (0/2) (0/2) (2/2) (2/2) True False True +ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) (0/1) True False True +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 (0/1) (0/1) (0/1) (0/1) True False True +eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (3/3) (3/3) (3/3) (3/3) True False True +emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) (107/107) True False True +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) (7/7) True False True +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) (1/1) True False True +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 (0/1) (0/1) (0/1) (0/1) True False True +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) (0/1) True False True +fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 (0/1) (0/1) (1/1) (1/1) True False True +fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 (0/1) (0/1) (1/1) (0/1) True False True +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 (1/1) (1/1) (1/1) (1/1) True False True +fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) True False True +fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) True False True +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) True False True +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False True +filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) (1/1) True False True +flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) (0/1) True False True +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.4 (1/1) (1/1) (1/1) (1/1) True False True +format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 (0/1) (0/1) (1/1) (0/1) True False True +fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 (0/1) (1/1) (1/1) (1/1) True False True +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.4.4 freyja 1.5.0 (2/4) (0/4) (4/4) (0/4) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) (5/5) True False True +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) (0/1) True False True +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) (5/5) True False True +gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) (0/8) True False True +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) (0/1) True False True +goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) (2/2) True False True +goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) (1/1) True False True +graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 (2/2) (2/2) (2/2) (2/2) True False True +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) (0/2) True False True +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.3.2 gtdbtk 2.4.0 (0/1) (1/1) (1/1) (0/1) True False True +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 (1/1) (1/1) (1/1) (0/1) True False True +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) True False True +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) True False True +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) True False True +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) (0/1) True False True +hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 (0/12) (12/12) (12/12) (12/12) True False True +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.8 humann 3.8 (6/13) (12/13) (13/13) (13/13) True False True +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 (17/17) (2/17) (17/17) (2/17) True False True +hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) (0/1) True False True +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 (0/1) (0/1) (0/1) (0/1) True False True +idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) (3/3) True False True +infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 (0/6) (6/6) (6/6) (0/6) True False True +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 (0/2) (0/2) (2/2) (0/2) True False True +integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.3 integron_finder 2.0.3 (0/1) (1/1) (1/1) (1/1) True False True +interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) (1/1) True False True +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) (0/1) True False True +iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.4 iqtree 2.3.4 (1/1) (1/1) (1/1) (0/1) True False True +isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) (1/1) True False True +itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) (0/1) True False True +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) (5/5) True False True +jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) (2/2) True False True +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) (1/1) True False True +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) True False True +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) (0/1) True False True +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) (0/8) True False True +kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) (0/1) True False True +kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) (1/1) True False True +kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) True False True +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) True False True +kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk (1/1) (1/1) (1/1) (0/1) True False True +kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) (1/1) True False True +kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (1/1) (1/1) (0/1) True False True +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 (1/6) (6/6) (6/6) (6/6) True False True +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (1/1) (0/1) True False True +lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) (0/1) True False True +lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 (0/1) (0/1) (1/1) (0/1) True False True +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) (1/1) True False True +lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base (0/1) (0/1) (1/1) (0/1) True False True +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) (0/1) True False True +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) (0/1) True False True +m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) (0/1) True False True +maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 0.99.12 maaslin2 1.16.0 (0/1) (0/1) (1/1) (0/1) True False True +mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.520 mafft 7.525 (2/2) (2/2) (2/2) (2/2) True False True +make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) (0/1) True False True +maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) True False True +mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) True False True +mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) True False True +maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) True False True +maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) (0/2) True False True +mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) True False True +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) (3/4) True False True +megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) True False True +megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (0/1) True False True +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) True False True +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) True False True +merqury 2483.0 244.0 merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 (2/2) (2/2) (2/2) (2/2) True False True +meryl 6785.0 350.0 meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 (0/7) (0/7) (0/7) (0/7) True False True +metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.15 (2/2) (1/2) (2/2) (2/2) True False True +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) True False True +metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) (0/1) True False True +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) True False True +metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) (0/1) True False True +metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.1 (1/4) (2/4) (4/4) (4/4) True False True +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) (0/6) True False True +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) True False True +minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) True False True +miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) True False True +minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) (0/1) True False True +miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) True False True +mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 (1/2) (1/2) (2/2) (0/2) True False True +mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) (2/2) True False True +mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) (2/2) True False True +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) (129/129) True False True +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) (0/1) True False True +msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) (1/1) True False True +msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) (0/1) True False True +multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) True False True +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.22.2 (1/1) (1/1) (1/1) (1/1) True False True +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) True False True +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base (0/1) (0/1) (0/1) (0/1) True False True +mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) (0/1) True False True +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) True False True +nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) True False True +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) True False True +ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) (16/18) True False True +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) True False True +newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) True False True +nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) True False True +nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) (0/1) True False True +nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) (1/1) True False True +nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) (0/1) True False True +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) True False True +obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) (1/2) True False True +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) True False True +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) True False True +orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) True False True +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) True False True +peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.6 (4/4) (4/4) (4/4) (4/4) True False True +pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) (1/1) True False True +pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " pharokka - " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " (0/1) (1/1) (1/1) True True -phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3) True True -phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) True True -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) True True -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) True True -plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) True True -plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) True True -polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) True False -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) True False -pretext pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext 0.1.9 pretextmap 0.1.9 (2/2) (2/2) (2/2) True False -prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) True False -progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) True False -prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) True True -prot-scriber prot_scriber Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber 0.1.4 prot-scriber 0.1.5 (0/1) (0/1) (1/1) True False -proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Homology-based gene prediction Phylogeny Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) True True -pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) True False -purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) True False -pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) True True -pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks 3.8 pygenometracks 3.8 (1/1) (1/1) (1/1) True True -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) True False -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/2) (0/2) (2/2) True True -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/32) (0/32) (32/32) True True -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) True False -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (3/4) (4/4) True True -quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) True True -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) True True -ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) True False -rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) True False -raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) True False -raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) True True -read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) True True -recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.13.2 recentrifuge 1.13.2 (0/1) (0/1) (1/1) True True -red 578.0 88.0 red Red (REpeat Detector) Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) True False -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) True False -repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) True False -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) True False -rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast 2.2.3 rnaquast 2.2.3 (0/1) (0/1) (1/1) True False -roary 12225.0 656.0 roary Roary the pangenome pipeline roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) True True -rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc 5.0.1 rseqc 5.0.3 (22/22) (22/22) (22/22) True True -ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) True False -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) True False -sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) True True -sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) True True -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) True False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (4/5) (5/5) True False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) True False -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) True False -scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) True True -scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) True False -semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin 2.0.2 semibin 2.0.2 (0/6) (0/6) (6/6) True True -seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) True False -seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) True False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.6.1 (0/3) (0/3) (3/3) True True -seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 1.2.1 seqsero2 1.2.1 (0/1) (0/1) (1/1) False -seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) True False -seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ 0.7.5 seqwish 0.7.9 (0/1) (0/1) (1/1) True False -seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) True False -shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) True False -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) True False -shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) True True -sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) True False -sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) True False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto 0.9.0 sinto 0.10.0 (2/2) (0/2) (2/2) True False -slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) True False -sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) True False -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 (0/1) (0/1) (1/1) True True -smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) True False -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) True True -sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc 1.0.12 sniffles 2.2 (1/1) (1/1) (1/1) True False -snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) True False -snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) True True -socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) True False -sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) True True -spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) True True -spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln 2.4.9 python (2/2) (0/2) (2/2) True False -spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine 2.1 spotyping 2.1 (0/1) (0/1) (1/1) True True -srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 0.2.0 samtools 1.19.2 (0/1) (0/1) (1/1) True True -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) True False -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) True False -star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.12.0 (1/1) (1/1) (1/1) True False -structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) True True -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) True False -syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) True False -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) True False -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) True False -taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) True True -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler 4.4.1 tb-profiler 5.0.1 (1/1) (1/1) (1/1) True True -tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) True False -te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ 1.0.1 samtools 1.19.2 (0/1) (0/1) (1/1) True False -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) True False -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) True False -tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) True False -tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) True False -transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) True False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 (5/5) (2/5) (5/5) True False -transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) True True -trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (11/13) (13/13) True False -trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) True False -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler 0.5.4 trycycler 0.5.4 (0/5) (5/5) (5/5) True False -tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra 1.1.2 tsebra 1.1.2.2 (0/1) (0/1) (1/1) True False -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l 377 ucsc-blat 445 (0/1) (0/1) (0/1) True False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 (5/5) (3/5) (5/5) True False -unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) True True -usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) True True -valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet valet 1.0 (1/1) (0/1) (1/1) True True -vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) True True -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP 1.1.1 varvamp 1.1.1 (0/1) (0/1) (0/1) False -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) True True -velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) True True -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) True True -verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko 1.3.1 verkko 1.4.1 (0/1) (0/1) (1/1) True False -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg 1.23.0 vg 1.54.0 (0/3) (0/3) (3/3) True False -volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) True False -vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch 2.8.3 vsearch 2.27.0 (8/8) (8/8) (8/8) True True -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp 3.0.6 pysam 0.22.0 (0/5) (0/5) (0/5) True False -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) True False -windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ 1.0 blast 2.15.0 (0/2) (2/2) (2/2) False -yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) True False -bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) True True -bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) True False -bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (0/4) (4/4) True False -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) True True -kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ kraken 1.1.1 (5/5) (5/5) (5/5) True True -kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) True True -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 (0/1) (1/1) (1/1) True False -bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) True False -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) True False -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) True False -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) True False -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) True False -dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) True False -decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) True False -dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) True False -dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) True False -diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN 1.8.1 (0/1) (1/1) (1/1) True False -diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) True False -diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation Up-to-date https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.6 (0/1) (0/1) (1/1) True False -data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager (0/1) (0/1) (0/1) True False -data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) True False -eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (1/3) (3/3) (3/3) True True -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) True False -fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) True False -feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) True False -filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) True False -flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) True False -hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) True False -idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) True False -lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) True False -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant 1.22.0 r-base (0/2) (2/2) (2/2) True False -map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) True False -maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) True False -meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) True False -metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator 1.0.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) True True -metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) True False -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) True False -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) True False -morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 287 (0/1) (1/1) (1/1) True False -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) True False -msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container To update Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) True False -msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2023.01.1202 (0/1) (0/1) (1/1) True False -msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) True False -msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) True False -msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) True False -mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse (0/1) (0/1) (1/1) True False -mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data To update Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) True False -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (1/164) (36/164) (160/164) True False -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) True False -pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) True False -pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) True False -pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) True False -peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp 1.0.0 python (1/1) (1/1) (1/1) True False -peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.5 (4/4) (4/4) (4/4) True False -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) True False -percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator 3.5 percolator 3.5 (0/4) (4/4) (4/4) True False -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) True False -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) True False -custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) True False -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db (0/1) (0/1) (0/1) True False -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) True False -translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) True False -proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) True False -proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) True False -proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) True False -proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) True False -proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) True False -proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) True False -proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) True False -proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) True False -proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) True False -proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python (0/1) (0/1) (0/1) True False -psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) True False -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) True False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.6.3 (0/1) (0/1) (1/1) True False -quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) True False -quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) True False -rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) True False -sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) True False -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) True False -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) True False -translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) True False -unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs 4.5.1 python (1/1) (1/1) (1/1) True False -uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) True False -validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) True False -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.0 (0/1) (0/1) (0/1) True False -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) True False -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) True False -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) True False -cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) True False -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) True False -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) True False -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) True False -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) True False -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) True False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats 0.19.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) True False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.5.1 tar (0/1) (1/1) (0/1) True False -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/oases 1.3.0 oases 0.2.09 (0/1) (0/1) (0/1) True False -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage 0.7.0 samtools 1.19.2 (0/1) (0/1) (0/1) True False -rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) True False -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) True False -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters 1.3.0 pysam 0.22.0 (0/1) (0/1) (0/1) True False -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) True False -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures 3.4.2 pysam 0.22.0 (0/2) (0/2) (0/2) True False -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) True False -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) True False -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) True False -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) True False -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) True False -EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) True False -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/5) (0/5) (5/5) True False -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) False -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy 0.0.2 (0/5) (5/5) (5/5) True True -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) True False -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) True False -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools 0.0.0 r-tangles (0/6) (0/6) (6/6) True False -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ 2022.3.0 xarray (5/6) (2/6) (6/6) True False -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) True False -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) False -obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) True True -ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) False -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) True False -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) True False -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) True False -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc 0.0.2 (0/5) (0/5) (5/5) True False -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) True False -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) True False -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) True False -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) True False -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) True False -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) True False -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.0 (1/1) (1/1) (1/1) True False -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) True False -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) True False -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) True False -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) True False -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) True False -dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) True False -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) True False -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) True False -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) True False -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy 1.8.1 scanpy-scripts 1.1.6 (17/27) (27/27) (27/27) True False -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) True False -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.6.3 scmap-cli 0.1.0 (0/7) (0/7) (7/7) True False -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) True False -seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.3.0 seurat-scripts 4.0.0 (0/13) (0/13) (12/13) True False -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) True False -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) True False -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy (0/1) (0/1) (0/1) True False -blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) False -blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) False -blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) False -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) False -ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) False + " (0/1) (1/1) (1/1) (0/1) True False True +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) True False True +phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) True False True +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) True False True +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) True False True +plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) True False True +plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) True False True +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 3.15.5 (0/1) (0/1) (0/1) (0/1) True False True +polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) True False True +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) True False True +prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) True False True +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python (0/1) (0/1) (0/1) (0/1) True False True +proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) (0/3) True False True +pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) True False True +pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 (1/1) (1/1) (1/1) (1/1) True False True +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 (0/2) (0/2) (2/2) (2/2) True False True +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 (0/32) (0/32) (32/32) (32/32) True False True +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (4/4) (4/4) (1/4) True False True +quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) (1/1) True False True +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) (0/1) True False True +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) True False True +racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) (1/1) True False True +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 0.8.0 rasusa 2.0.0 (0/1) (0/1) (1/1) (0/1) True False True +raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) (1/1) True False True +read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) (0/1) True False True +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (1/1) (0/1) True False True +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.14.0 recentrifuge 1.14.0 (0/1) (0/1) (1/1) (1/1) True False True +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) True False True +roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) True False True +rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing Up-to-date https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.3 (22/22) (22/22) (22/22) (22/22) True False True +salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) True False True +sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) True False True +sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) True False True +scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) (0/1) True False True +semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 (0/6) (0/6) (6/6) (1/6) True False True +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 (0/5) (2/5) (3/5) (2/5) True False True +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) True False True +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) True False True +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) True False True +shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) True False True +sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 (0/1) (1/1) (1/1) (0/1) True False True +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing To update https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.1 (0/1) (0/1) (1/1) (0/1) True False True +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) (0/1) True False True +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) (0/2) True False True +snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) (3/3) True False True +sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) True False True +sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) (1/1) True False True +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) True False True +spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) True False True +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) True False True +srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.20 (0/1) (0/1) (1/1) (0/1) True False True +srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) (0/1) True False True +staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) (1/1) True False True +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) (0/1) True False True +structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) (1/1) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 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qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, 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qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) True False True 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qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) True False True +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) True False True +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, 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https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True False True +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True False True +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, 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https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, 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qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +t2ps 457.0 31.0 Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) (0/1) True False True +taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) (1/1) True False True +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction Up-to-date https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.2.1 (1/1) (1/1) (1/1) (0/1) True False True +tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.8.5.0 tooldistillator 0.8.5.0 (0/2) (0/2) (2/2) (2/2) True False True +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) True False True +transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) True False True +trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) True False True +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) True False True +unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) (1/1) True False True +unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python (1/1) (1/1) (1/1) (0/1) True False True +uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) (0/1) True False True +usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) (0/2) True False True +valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 (1/1) (0/1) (1/1) (1/1) True False True +vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) (0/1) True False True +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.0 (0/1) (0/1) (1/1) (0/1) True False True +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3) True False True +velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) (2/2) True False True +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) True False True +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) True False True +vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.28.1 (8/8) (8/8) (8/8) (8/8) True False True +wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) (1/1) True False True diff --git a/results/microgalaxy/tools_filtered_by_ts_categories.tsv b/results/microgalaxy/tools_filtered_by_ts_categories.tsv new file mode 100644 index 00000000..db3d0d99 --- /dev/null +++ b/results/microgalaxy/tools_filtered_by_ts_categories.tsv @@ -0,0 +1,866 @@ +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr Reviewed Deprecated To keep +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) (9/9) True False False +Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/6) (0/6) (6/6) (5/6) True False False +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 (0/1) (0/1) (1/1) (0/1) True False False +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) (3/3) True False False +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) (0/2) True False False +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 (0/5) (5/5) (5/5) (5/5) True False True +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) (0/1) True False False +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) True False False +ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.4 (0/1) (1/1) (1/1) (0/1) True False False +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) (0/1) True False True +TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) (0/1) True False False +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) (1/1) True False True +abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) True False True +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) True False True +abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.7 abyss 2.3.7 (0/1) (1/1) (1/1) (0/1) True False True +adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) (0/1) True False False +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) (4/4) True False False +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) (0/1) True False True +align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False False +amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) (0/1) True False True +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.6 (0/19) (0/19) (19/19) (0/19) True False False +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) (1/1) True False True +ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) (0/1) True False True +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.3 anndata 0.6.22.post1 (5/5) (4/5) (5/5) (0/5) True False False +annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) (1/1) True False False +antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) (0/1) True False False +antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 (1/1) (1/1) (1/1) (0/1) True False True +aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 (0/1) (0/1) (1/1) (0/1) False +aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) (0/1) True False False +arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) (0/3) True False False +art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (3/3) (0/3) True False False +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) (0/2) True False True +assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) (1/1) True False False +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False True +augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) (1/1) True False False +augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) (2/2) True False False +b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) (0/1) True False False +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.3 bakta 1.9.3 (0/1) (1/1) (1/1) (1/1) True False True +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl (0/1) (0/1) (0/1) (0/1) True False False +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) (0/1) True False False +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) True False False +bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) True False True +bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) (1/1) True False False +bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (2/4) (4/4) (0/4) True False False +bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) (0/2) True False False +bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) (2/2) True False True +barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) True False False +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 (4/4) (0/4) (4/4) (0/4) True False False +barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) (1/1) True False False +bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) (0/1) True False False +bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) (0/1) True False True +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) (0/6) True False True +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) (0/7) True False False +bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) (0/1) True False False +bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) (0/1) True False False +best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) (1/1) True False False +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 (0/1) (0/1) (1/1) (0/1) True False True +binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) (0/1) True False True +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) (0/1) True False True +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python (1/1) (0/1) (1/1) (0/1) True False False +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (6/6) (0/6) True False True +bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) (0/1) True False False +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) (1/1) True False False +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) True False True +biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) (0/1) True False False +bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (4/4) (4/4) (4/4) True False False +blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) (0/1) True False True +blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) (0/1) True False False +blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) (0/1) True False False +blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False True +blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) (0/1) True False False +blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) (0/1) True False False +blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) (0/1) True False False +blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (0/1) True False False +blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) (0/1) True False True +blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) (0/1) True False False +blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) (0/1) True False False +blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) (0/1) True False False +bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (1/1) (1/1) (1/1) (1/1) True False True +braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) (0/1) True False False +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 (0/1) (1/1) (1/1) (1/1) True False False +bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) (0/5) True False False +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) (1/1) True False False +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) True False True +bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) True False False +cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) True False False +calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) (0/1) True False False +calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) (0/1) True False False +cami_amber cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.4 cami-amber 2.0.4 (0/3) (0/3) (0/3) (0/3) False +cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) (0/1) True False False +cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) (11/11) True False False +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) True False True +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) (0/1) True False True +cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) True False True +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) (0/8) True False False +cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) (0/1) True False True +champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) (3/3) True False False +charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt (0/1) (0/1) (0/1) (0/1) True False False +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) (10/10) True False True +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) (0/2) True False False +chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) (0/1) True False False +chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) (0/5) True False False +chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) (1/1) True False False +chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) (0/1) True False False +circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) (0/1) True False False +circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) True False False +clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 0.1.12 clair3 1.0.8 (0/1) (0/1) (1/1) (0/1) True False True +clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.20 (0/2) (0/2) (0/2) (0/2) True False False +climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) (0/1) True False False +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) (0/1) True False True +clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) True False True +cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl (0/1) (0/1) (1/1) (0/1) True False True +cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) (0/4) True False False +codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) True False True +cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) (0/1) True False False +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) True False True +colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) True False False +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) True False False +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk (1/1) (1/1) (1/1) (1/1) True False False +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 (0/1) (0/1) (0/1) (0/1) True False False +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) (0/1) True False True +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python (0/1) (0/1) (1/1) (0/1) True False True +combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 (0/1) (0/1) (0/1) (0/1) True False False +compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 (0/1) (0/1) (1/1) (0/1) True False False +compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) (0/1) True False True +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) True False True +compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) (0/1) True False False +compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) (0/1) True False False +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) True False True +consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) (1/1) True False False +consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) (0/1) True False False +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis cosg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 (0/1) (0/1) (0/1) (0/1) False +count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) (1/1) True False False +count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.20 (0/1) (0/1) (0/1) (0/1) True False False +coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) (0/1) True False False +coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) True False False +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) True False True +crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) (0/1) True False False +crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) (0/1) True False False +crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) (0/1) True False False +cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) (0/1) True False True +ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) (0/1) True False False +cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) (0/1) True False False +custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) (1/1) True False False +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager (0/1) (0/1) (0/1) (0/1) True False False +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.8 cutadapt 4.8 (1/1) (1/1) (1/1) (1/1) True False True +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) True False True +das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 (0/2) (0/2) (2/2) (2/2) True False True +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) (0/1) True False False +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) (1/1) True False False +data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles (0/6) (0/6) (6/6) (6/6) True False False +data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper (0/1) (0/1) (0/1) (0/1) True False False +data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) (0/1) True False False +dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) (1/1) True False False +decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) (0/1) True False False +deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) (1/1) True False False +delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) (0/1) True False False +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) True False True +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) (0/1) True False False +dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) (0/1) True False False +dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) True False False +dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) (0/1) True False False +dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) (0/1) True False False +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) True False True +diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 (0/1) (1/1) (1/1) (0/1) True False False +diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) (0/1) True False False +diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 (0/1) (0/1) (1/1) (0/1) True False False +disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 (1/1) (0/1) (1/1) (0/1) True False True +divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) (0/1) True False False +dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 (0/1) (0/1) (1/1) (0/1) True False False +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 (0/1) (0/1) (0/1) (0/1) True False False +dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) (0/1) True False False +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.3.5 dram 1.5.0 (0/5) (0/5) (5/5) (0/5) True False True +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 (0/2) (0/2) (2/2) (2/2) True False True +droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) (0/1) True False False +dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) (1/1) True False False +dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) (0/2) True False False +ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) (0/1) True False True +edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 (1/1) (1/1) (1/1) (1/1) True False False +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 (0/1) (0/1) (0/1) (0/1) True False True +eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (3/3) (3/3) (3/3) (3/3) True False True +egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) (0/1) True False False +emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) (107/107) True False True +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) (0/7) True False False +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) (7/7) True False True +exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) (0/1) True False False +exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) (1/1) True False False +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) (0/1) True False False +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) (1/1) True False True +express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) (0/1) True False False +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 (0/1) (0/1) (0/1) (0/1) True False True +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) (0/1) True False True +fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) True False False +fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy (1/1) (1/1) (1/1) (1/1) True False False +fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 (0/1) (0/1) (1/1) (1/1) True False True +fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) (0/2) True False False +fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 (0/1) (0/1) (1/1) (0/1) True False True +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 (1/1) (1/1) (1/1) (1/1) True False True +fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) (0/1) True False False +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) (0/2) True False False +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) True False True +fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) True False True +feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) (0/1) True False False +featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) True False False +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) True False True +feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (1/1) (1/1) (1/1) True False False +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) (0/1) True False False +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) (0/2) True False False +fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) (1/1) True False False +filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) (1/1) True False False +filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False True +filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) (1/1) True False False +filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) (1/1) True False True +find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False False +find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) (0/1) True False False +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) (0/2) True False False +flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) (0/1) True False False +flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) (0/1) True False True +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.4 (1/1) (1/1) (1/1) (1/1) True False True +format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 (0/1) (0/1) (1/1) (0/1) True False True +fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 (0/1) (1/1) (1/1) (1/1) True False True +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.4.4 freyja 1.5.0 (2/4) (0/4) (4/4) (0/4) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True False True +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) (5/5) True False True +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) (0/7) True False False +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) (1/1) True False False +gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) (8/8) True False False +gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) (0/1) True False False +gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) (2/3) True False False +geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) (0/1) True False False +generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) (1/1) True False False +genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) (0/1) True False False +get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) (1/1) True False False +getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) True False False +getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) (0/1) True False False +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) (0/1) True False True +getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 (0/2) (2/2) (2/2) (0/2) True False False +gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) (0/1) True False False +gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (1/1) True False False +gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) (1/1) True False False +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) (5/5) True False True +gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) (0/8) True False True +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) (0/1) True False True +gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) (1/1) True False False +goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) (2/2) True False True +goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) (1/1) True False True +gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) (0/1) True False False +graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) (0/1) True False False +graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 (2/2) (2/2) (2/2) (2/2) True False True +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) (0/2) True False True +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) (0/1) True False False +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) True False False +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.3.2 gtdbtk 2.4.0 (0/1) (1/1) (1/1) (0/1) True False True +gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 (1/1) (1/1) (1/1) (0/1) True False False +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 (1/1) (1/1) (1/1) (0/1) True False True +guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) (0/1) True False False +gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) (0/1) True False False +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) True False True +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) True False True +hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 (0/1) (1/1) (0/1) (0/1) True False False +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) True False False +hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) (0/2) True False False +hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) (0/1) True False False +hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) (0/1) True False False +heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.1.3.1 r-gplots 2.17.0 (1/1) (1/1) (1/1) (1/1) True False False +heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) True False False +helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 (0/1) (0/1) (1/1) (1/1) True False False +hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) (0/1) True False False +hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) (0/1) True False False +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.2 hicexplorer 3.7.4 (0/40) (5/40) (40/40) (4/40) True False False +hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.1.5 hicstuff 3.2.2 (0/1) (0/1) (0/1) (0/1) True False False +hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.9 (1/1) (1/1) (1/1) (1/1) True False False +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) True False True +high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) (0/1) True False False +hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) (0/1) True False False +hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) (1/1) True False False +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) (0/1) True False True +hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 (0/12) (12/12) (12/12) (12/12) True False True +homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) (4/5) True False False +homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) (0/1) True False False +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) (0/1) True False False +htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 (1/1) (1/1) (1/1) (1/1) True False False +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.8 humann 3.8 (6/13) (12/13) (13/13) (13/13) True False True +hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.1.7 (0/1) (1/1) (1/1) (0/1) True False False +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 (17/17) (2/17) (17/17) (2/17) True False True +hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) (0/1) True False True +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 (0/1) (0/1) (0/1) (0/1) True False True +idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) (3/3) True False True +idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) (0/1) True False False +idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) (0/1) True False False +iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) (0/1) True False False +illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) (0/1) True False False +improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) (0/1) True False False +indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) (0/1) True False False +infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 (0/6) (6/6) (6/6) (0/6) True False True +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) (0/1) True False False +instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) (0/1) True False False +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 (0/2) (0/2) (2/2) (0/2) True False True +intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) (0/1) True False False +integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.3 integron_finder 2.0.3 (0/1) (1/1) (1/1) (1/1) True False True +interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) (0/1) True False False +interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) (1/1) True False True +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) (0/1) True False True +iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.4 iqtree 2.3.4 (1/1) (1/1) (1/1) (0/1) True False True +isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) (1/1) True False True +isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) (1/1) True False False +isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) (1/1) True False False +itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) (0/1) True False True +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) (5/5) True False True +jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) (2/2) True False True +jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.11 (1/1) (1/1) (1/1) (1/1) True False False +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) (1/1) True False True +kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b1 (0/1) (0/1) (0/1) (0/1) True False False +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) True False True +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) (0/1) True False True +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) (0/8) True False True +kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) (0/1) True False False +kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) (0/1) True False True +kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) (1/1) True False True +kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) True False True +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) True False True +kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk (1/1) (1/1) (1/1) (0/1) True False True +kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) (1/1) True False True +kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (1/1) (1/1) (0/1) True False True +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 (1/6) (6/6) (6/6) (6/6) True False True +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (1/1) (0/1) True False True +labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) (0/1) True False False +last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1542 (0/5) (0/5) (5/5) (5/5) True False False +lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) (0/1) True False True +length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) (1/1) True False False +lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) (0/1) True False False +lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 (0/1) (0/1) (1/1) (0/1) True False True +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) (1/1) True False True +lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base (0/1) (0/1) (1/1) (0/1) True False True +links 405.0 77.0 links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) (0/1) True False False +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) (0/5) True False False +logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) (0/1) True False False +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) (0/1) True False True +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) (0/1) True False True +m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) (0/1) True False True +maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 0.99.12 maaslin2 1.16.0 (0/1) (0/1) (1/1) (0/1) True False True +macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) (9/9) True False False +maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) True False False +mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.520 mafft 7.525 (2/2) (2/2) (2/2) (2/2) True False True +make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) (0/1) True False True +maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) True False True +maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base (0/2) (2/2) (2/2) (2/2) True False False +map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False False +mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) True False False +mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) True False True +mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) True False True +mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) True False False +masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) (0/1) True False False +mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) (0/1) True False False +maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) True False True +maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) (0/2) True False True +mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) True False True +mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) (0/1) True False False +mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) (0/1) True False False +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) (3/4) True False True +medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas (0/1) (0/1) (1/1) (0/1) True False False +megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) True False True +megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (0/1) True False True +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) True False True +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) True False True +merqury 2483.0 244.0 merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 (2/2) (2/2) (2/2) (2/2) True False True +meryl 6785.0 350.0 meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 (0/7) (0/7) (0/7) (0/7) True False True +meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) (0/1) True False False +metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.15 (2/2) (1/2) (2/2) (2/2) True False True +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) True False True +metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) (0/1) True False True +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) True False True +metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) (0/1) True False True +metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.1 (1/4) (2/4) (4/4) (4/4) True False True +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) (0/6) True False True +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) True False True +methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) (0/8) True False False +methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) (0/1) True False False +metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) (1/1) True False False +mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 (0/1) (0/1) (0/1) (0/1) False +miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) (0/1) True False False +microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) (0/1) True False False +microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) True False False +migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) True False False +minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) (0/1) True False False +minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) True False True +miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) True False True +minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) (0/1) True False True +miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) True False True +miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) (1/1) True False False +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar (0/1) (1/1) (0/1) (0/1) True False False +mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) True False False +mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) True False False +mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) (0/1) True False False +mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (1/1) (1/1) (0/1) True False False +mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 (1/2) (1/2) (2/2) (0/2) True False True +mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) (2/2) True False True +moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) (0/1) True False False +mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) (2/2) True False True +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) (0/9) True False False +morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 288 (0/1) (1/1) (1/1) (0/1) True False False +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) (129/129) True False True +mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 (0/1) (0/1) (1/1) (0/1) True False False +mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) (0/2) True False False +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) (0/1) True False True +msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) (1/1) True False True +msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 (0/1) (0/1) (1/1) (0/1) True False False +msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) (1/1) True False False +msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) (0/1) True False False +msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) (0/1) True False True +mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse (0/1) (0/1) (1/1) (0/1) True False False +multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) True False True +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.22.2 (1/1) (1/1) (1/1) (1/1) True False True +multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) (0/1) True False False +mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) (0/1) True False False +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) (6/6) True False False +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) True False True +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base (0/1) (0/1) (0/1) (0/1) True False True +mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) (0/1) True False True +mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) (0/1) True False False +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) (0/3) True False False +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) True False True +nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) True False True +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) True False True +nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) (0/1) True False False +ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) (16/18) True False True +ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) True False False +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) True False True +necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) (0/1) True False False +newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) True False True +nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) True False True +nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) (0/1) True False True +nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) (0/1) True False False +nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) (1/1) True False True +novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 (0/1) (1/1) (1/1) (1/1) True False False +nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) (0/1) True False True +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) True False True +oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 (0/1) (0/1) (0/1) (0/1) True False False +obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) (1/2) True False True +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) True False True +ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) (0/1) True False False +odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.8.6 (0/2) (0/2) (2/2) (2/2) True False False +ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base (0/1) (0/1) (1/1) (0/1) True False False +ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base (0/1) (0/1) (1/1) (0/1) True False False +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) True False True +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4) (0/4) True False False +openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (8/164) (35/164) (160/164) (0/164) True False False +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (7/140) (34/140) (135/140) (0/140) True False False +optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) (0/1) True False False +orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) True False True +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) True False True +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 (5/5) (0/5) (5/5) (0/5) True False False +pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) True False False +pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) True False False +paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) (0/1) True False False +parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) True False False +pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) True False False +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) (0/1) True False False +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python (0/1) (0/1) (0/1) (0/1) True False False +peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) (0/1) True False False +pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) (0/1) True False False +pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) (0/1) True False False +pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) (0/3) True False False +peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python (1/1) (1/1) (1/1) (0/1) True False False +peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.6 (4/4) (4/4) (4/4) (4/4) True False True +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 (0/4) (0/4) (0/4) (0/4) True False False +pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) (0/1) True False False +percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.6.5 (0/4) (4/4) (4/4) (0/4) True False False +pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) (1/1) True False True +pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " + pharokka + " (0/1) (1/1) (1/1) (0/1) True False True +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) True False True +phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) True False True +pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) (0/3) True False False +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) True False True +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) True False True +pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) (0/1) True False False +piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) (0/1) True False False +plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) True False True +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite (0/1) (0/1) (0/1) (0/1) True False False +plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) True False True +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 3.15.5 (0/1) (0/1) (0/1) (0/1) True False True +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) (0/1) True False False +plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.3 galaxy-ml 0.10.0 (1/1) (1/1) (1/1) (0/1) True False False +plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) (0/1) True False False +plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) (0/1) True False False +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) (0/1) True False False +poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 (0/1) (1/1) (1/1) (0/1) True False False +polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) True False True +predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) (0/1) True False False +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) (0/11) True False False +pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 (3/3) (2/3) (3/3) (0/3) True False False +prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) (1/1) True False False +probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) True False False +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) True False True +progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) (0/2) True False False +prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) True False True +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python (0/1) (0/1) (0/1) (0/1) True False True +prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.5 prot-scriber 0.1.5 (0/1) (0/1) (1/1) (0/1) True False False +protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) (0/1) True False False +protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) (0/6) True False False +protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False False +proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) (0/3) True False True +proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) (0/1) True False False +proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) (0/1) True False False +proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python (0/1) (0/1) (0/1) (0/1) True False False +pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) (1/1) True False False +psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) (0/1) True False False +psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) (0/1) True False False +pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) (0/1) True False False +purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) (0/1) True False False +pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) True False True +pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 (1/1) (1/1) (1/1) (1/1) True False True +pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) (0/6) True False False +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) (0/1) True False False +pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.2 (0/1) (0/1) (1/1) (0/1) True False False +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 (0/2) (0/2) (2/2) (2/2) True False True +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 (0/32) (0/32) (32/32) (32/32) True False True +qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip (0/1) (0/1) (1/1) (0/1) False +qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) (0/1) True False False +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (4/4) (4/4) (1/4) True False True +quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.11.0 (0/1) (0/1) (0/1) (0/1) True False False +quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) (1/1) True False False +quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) (0/1) True False False +quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) (12/12) True False False +quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) (1/1) True False True +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) (0/1) True False True +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) True False True +racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) (1/1) True False True +ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) (1/1) True False False +rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) (1/1) True False False +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 0.8.0 rasusa 2.0.0 (0/1) (0/1) (1/1) (0/1) True False True +raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 (0/1) (1/1) (1/1) (1/1) True False False +rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) (0/1) True False False +raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) (1/1) True False True +rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) True False False +rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) (0/1) True False False +rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) (0/1) True False False +read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) (0/1) True False True +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (1/1) (0/1) True False True +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.14.0 recentrifuge 1.14.0 (0/1) (0/1) (1/1) (1/1) True False True +red 578.0 88.0 red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) (1/1) True False False +refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) (2/2) True False False +regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) (7/7) True False False +remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) (0/1) True False False +repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) (1/1) True False False +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) True False True +repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) (1/1) True False False +repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) (1/1) True False False +revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) True False False +ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) (0/3) True False False +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) (0/2) True False False +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) (0/1) True False False +rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) (0/1) True False False +rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) (0/1) True False False +rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) (0/1) True False False +rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) (0/1) True False False +rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.2.3 rnaquast 2.2.3 (1/1) (0/1) (1/1) (1/1) True False False +rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) (0/1) True False False +rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) (0/6) True False False +roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) True False True +rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) (0/4) True False False +rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing Up-to-date https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.3 (22/22) (22/22) (22/22) (22/22) True False True +ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) (0/1) True False False +sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) (1/1) True False False +salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) True False True +salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) (0/1) True False False +salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) (0/1) True False False +sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) (1/1) True False False +samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.20 (0/1) (0/1) (0/1) (0/1) True False False +samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.20 (1/1) (1/1) (1/1) (1/1) True False False +samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.20 (1/1) (1/1) (1/1) (1/1) True False False +sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) True False True +sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) True False True +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) (0/1) True False False +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) (0/7) True False False +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 (17/27) (27/27) (27/27) (0/27) True False False +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) (0/6) True False False +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (5/5) (5/5) (0/5) True False False +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) (0/6) True False False +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) (0/16) True False False +scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) (0/1) True False False +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 (0/7) (0/7) (7/7) (0/7) True False False +scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) (0/1) True False True +scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) (0/1) True False False +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) (0/4) True False False +sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base (0/1) (0/1) (0/1) (0/1) True False False +selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) (0/1) True False False +semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 (0/6) (0/6) (6/6) (1/6) True False True +seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) (0/1) True False False +seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) (1/1) True False False +seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) (1/1) True False False +seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False False +seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) (0/1) True False False +seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False False +seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) (0/1) True False False +seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) (0/1) True False False +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 (0/5) (2/5) (3/5) (2/5) True False True +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) True False True +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) True False True +seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) (15/15) True False False +seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) (0/1) True False False +seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.10 (0/1) (0/1) (1/1) (0/1) True False False +seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) True False False +seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (14/19) (11/19) True False False +shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.12.0 (0/1) (1/1) (1/1) (0/1) True False False +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) True False True +short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) (0/1) True False False +short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) (0/1) True False False +shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) True False True +sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) (1/1) True False False +sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) (0/1) True False False +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.9.0 sinto 0.10.1 (2/2) (0/2) (2/2) (0/2) True False False +sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 (0/1) (1/1) (1/1) (0/1) True False True +sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) (0/4) True False False +slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) (0/2) True False False +sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) (0/1) True False False +small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) True False False +small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) (0/1) True False False +small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 (0/2) (0/2) (0/2) (0/2) True False False +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing To update https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.1 (0/1) (0/1) (1/1) (0/1) True False True +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) (0/1) True False True +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) True False False +smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) (0/1) True False False +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) (0/2) True False True +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Epigenetics, Sequence Analysis snapatac2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.5.3 (0/4) (0/4) (4/4) (0/4) False +sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 1.0.12 sniffles 2.3.3 (1/1) (1/1) (1/1) (1/1) True False False +snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) (0/1) True False False +snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) (3/3) True False True +snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) (0/1) True False False +sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) True False True +sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) (1/1) True False True +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) True False True +spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python (2/2) (0/2) (2/2) (0/2) True False False +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) (0/1) True False False +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) True False False +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) True False False +spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) (1/1) True False False +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred (0/1) (0/1) (0/1) (0/1) True False False +spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) True False True +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) True False True +sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) True False False +srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) (7/7) True False False +srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) (0/1) True False True +srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.20 (0/1) (0/1) (1/1) (0/1) True False True +sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) (0/1) True False False +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) (12/13) True False False +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) (12/12) True False False +star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 (1/1) (1/1) (1/1) (0/1) True False False +staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) (1/1) True False True +stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 (0/5) (0/5) (5/5) (5/5) True False False +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) (0/1) True False True +structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) (1/1) True False True +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) (0/1) True False False +substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) (0/1) True False False +substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) True False False +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True False True +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, 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qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To 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qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) True False True +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, 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qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True False True +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, 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https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True False True +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, 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qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True False True +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl (0/1) (0/1) (0/1) (0/1) True False False +syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) (0/1) True False False +t2ps 457.0 31.0 Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) True False True +t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) (0/1) True False True +tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) True False False +tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) (0/1) True False False +targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) (0/1) True False False +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) (0/1) True False False +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) (0/1) True False False +taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) (1/1) True False True +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction Up-to-date https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.2.1 (1/1) (1/1) (1/1) (0/1) True False True +tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) (1/1) True False False +te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.20 (0/1) (0/1) (1/1) (0/1) True False False +telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) (0/1) True False False +tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) (0/1) True False False +tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) (0/1) True False False +tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) (0/1) True False False +tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara (0/1) (0/1) (0/1) (0/1) False +tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.6 tn93 1.0.14 (4/4) (0/4) (4/4) (0/4) True False False +tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.8.5.0 tooldistillator 0.8.5.0 (0/2) (0/2) (2/2) (2/2) True False True +tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) True False False +tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 (1/1) (1/1) (1/1) (0/1) True False False +transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) (1/1) True False False +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) True False True +translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) (0/1) True False False +translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) True False False +transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) True False True +trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) True False True +trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) True False False +trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) True False False +trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) (0/2) True False False +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) True False True +tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.5 (0/1) (0/1) (1/1) (1/1) True False False +ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 377 ucsc-blat 445 (0/1) (0/1) (0/1) (0/1) True False False +ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) (0/1) True False False +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.2 umi_tools 1.1.5 (5/5) (5/5) (5/5) (5/5) True False False +unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) (1/1) True False True +unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python (1/1) (1/1) (1/1) (0/1) True False True +uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.5 requests (1/1) (1/1) (1/1) (0/1) True False False +uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) (0/1) True False True +usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) (0/2) True False True +valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 (1/1) (0/1) (1/1) (1/1) True False True +validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) (0/1) True False False +vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) (0/1) True False True +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.0 (0/1) (0/1) (1/1) (0/1) True False True +vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3) True False True +velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) (2/2) True False True +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) True False True +venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) (1/1) True False False +verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) True False False +verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.1 (0/1) (0/1) (1/1) (0/1) True False False +vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.56.0 (0/3) (0/3) (3/3) (3/3) True False False +vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) (0/23) True False False +vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) (4/4) True False False +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) True False True +virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7 virheat 0.7 (0/1) (0/1) (0/1) (0/1) False +volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) (1/1) True False False +vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.28.1 (8/8) (8/8) (8/8) (8/8) True False True +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 (0/5) (0/5) (0/5) (0/5) True False False +vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) (0/1) True False False +wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) (0/1) True False False +weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) (0/1) True False False +weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) (0/1) True False False +windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) True False False +windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) True False False +wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) (1/1) True False True +xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray (5/6) (2/6) (6/6) (5/6) True False False +xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) (0/2) True False False +yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) (0/1) True False False +yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) (0/1) True False False +zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. 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"https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null + } +] \ No newline at end of file diff --git a/results/repositories01.list_tools.tsv b/results/repositories01.list_tools.tsv index e0d18d96..d5cf882a 100644 --- a/results/repositories01.list_tools.tsv +++ b/results/repositories01.list_tools.tsv @@ -1,153 +1,140 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu -askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 (0/1) (0/1) (0/1) -baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 (0/2) (0/2) (0/2) -braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) -braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.6 (0/1) (1/1) (1/1) -feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest 0.1.0 openjdk (0/1) (0/1) (0/1) -get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python (0/1) (0/1) (0/1) -helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 (0/1) (0/1) (1/1) -logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) -meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 (0/1) (0/1) (0/1) -miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl (0/1) (0/1) (0/1) -openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest 0.1.0 openjdk (0/1) (0/1) (0/1) -peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest 2.0 (0/4) (0/4) (0/4) -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests (0/3) (0/3) (3/3) -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ 0.3.1 (0/1) (0/1) (1/1) -TreeBest treebest_best TreeBeST best To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) -apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ 1.0+galaxy1 apoc 1b16 (1/1) (0/1) (1/1) -blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) -ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ 0.0.2 EXPORT_DIR_PREFIX (0/1) (0/1) (0/1) -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) -gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python (0/1) (0/1) (1/1) -hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) -hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) -lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) -miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 (0/1) (0/1) (0/1) -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ 1.0 rDock 2013.1 (0/1) (0/1) (0/1) -replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ 0.1 python (0/1) (0/1) (1/1) -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 (0/1) (0/1) (0/1) -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ 1.0 smina 2017.11.9 (1/1) (0/1) (1/1) -t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) -abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) -assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl (0/1) (0/1) (0/1) -bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) -biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) -biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml 0.2.0 pandas (0/1) (0/1) (0/1) -bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) -collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml 5.1.0 gawk (1/1) (1/1) (1/1) -combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml 0.1 (0/1) (0/1) (0/1) -combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) -combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml 0.1 (0/1) (0/1) (0/1) -concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat 0.2 (0/1) (0/1) (0/1) -cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) -csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk 0.20.0 csvtk 0.29.0 (0/20) (0/20) (0/20) -ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) -fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) -filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) -gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 (0/1) (0/1) (0/1) -hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) -kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml 0.3.0 kaptive 2.0.6 (0/1) (0/1) (0/1) -kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml 2.3 kat 2.4.2 (0/1) (0/1) (0/1) -kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml 2.3 kat 2.4.2 (0/1) (0/1) (0/1) -mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) -mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite 3.0.3 mob_suite 3.1.8 (0/2) (2/2) (2/2) -mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) -mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base (0/1) (0/1) (0/1) -pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) -patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist 0.1.2 python (0/1) (0/1) (0/1) -plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml 0.1.6 r (0/1) (0/1) (0/1) -plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml (0/1) (0/1) (0/1) -plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml 1.1 spades 3.15.5 (0/1) (0/1) (0/1) -pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 (0/1) (0/1) (0/1) -promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer 1.2 python (0/1) (0/1) (0/1) -pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) -refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) -seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) -sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool Up-to-date https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml 1.1.1 sistr_cmd 1.1.1 (0/1) (1/1) (1/1) -smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) -spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools 1.1.2+galaxy1 sed (0/1) (0/1) (0/1) -spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) -spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml 1.0.1 spolpred (0/1) (0/1) (0/1) -srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) -staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) -stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) -tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. To update Text Manipulation tree_relabeler nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) -wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics 1.48.0 r-snow 0.4_1 (1/2) (2/2) (2/2) -correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ 1.0.1+galaxy0 r-batch 1.1_4 (0/1) (0/1) (0/1) -genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ genform r8 (0/1) (0/1) (1/1) -influx_si influx_si metabolic flux estimation based on [in]stationary labeling Up-to-date https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ 7.0.1 influx_si 7.0.1 (0/1) (0/1) (0/1) -ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO 1.10.0 bioconductor-ipo 1.28.0 (0/2) (0/2) (0/2) -isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) -kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ 1.0.0 python (0/1) (0/1) (0/1) -mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics 3.1.0 r-lme4 (0/1) (0/1) (0/1) -ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics 2.2.1 r-base (0/1) (0/1) (0/1) -nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation 3.0.0 r-batch 1.1_4 (0/1) (0/1) (1/1) -nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics 2.0.0 r-batch 1.1_4 (0/1) (0/1) (0/1) -nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing r-batch 1.1_4 (0/2) (2/2) (2/2) -normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization 1.0.7 r-batch 1.1_4 (0/1) (1/1) (1/1) -physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes Up-to-date physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit 3.3.2 physiofit 3.3.2 (0/1) (0/1) (0/1) -physiofit_manager physiofit_data_manager Handling of physiofit input files Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics 1.0.1 physiofit_data_manager 1.0.1 (0/1) (0/1) (0/1) -xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram To update https://github.com/sneumann/xcms Metabolomics xcms workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/ 3.12.0 bioconductor-xcms 4.0.0 (9/10) (9/10) (10/10) -apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 (0/9) (0/9) (9/9) -askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 (0/1) (0/1) (0/1) -chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 (0/26) (0/26) (0/26) -genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io To update https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.9 genoboo 0.4.12 (0/1) (0/1) (1/1) -jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python (0/1) (0/1) (0/1) -repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) -tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal To update https://github.com/galaxy-genome-annotation/python-tripal Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal python-tripal 3.2.1 (0/22) (0/22) (0/22) -w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master 0.98.18 r-base (0/1) (1/1) (1/1) -w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master 0.98.19 r-base (0/1) (1/1) (1/1) -w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master 0.98.2 coreutils 8.25 (0/1) (1/1) (1/1) -2d_auto_threshold 6541.0 39.0 ip_threshold Automatic thresholding scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) -2d_feature_extraction 13760.0 19.0 ip_2d_feature_extraction 2D feature extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_feature_extraction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ 0.1.1-2 pandas (0/1) (1/1) (1/1) -2d_filter_segmentation_by_features 6834.0 18.0 ip_2d_filter_segmentation_by_features filter segmentation by rules galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_filter_segmentation_by_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) -2d_histogram_equalization 656.0 39.0 ip_histogram_equalization 2d histogram equalization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging 2d_histogram_equalization imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ 0.0.1-2 scikit-image (0/1) (1/1) (1/1) -2d_simple_filter 6156.0 35.0 ip_filter_standard 2d simple filter scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_simple_filter imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ 0.0.3-3 scikit-image (0/1) (1/1) (1/1) -3d_tensor_feature_dimension_reduction ip_3d_tensor_feature_dimension_reduction Dimensionality reduction for features (channels) of 3D tensor data using UMAP To update https://github.com/BMCV/galaxy-image-analysis Imaging 3d_tensor_feature_dimension_reduction imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ 0.0.1 numpy (0/1) (0/1) (0/1) -anisotropic_diffusion 40.0 ip_anisotropic_diffusion Anisotropic image diffusion To update https://github.com/bmcv Imaging anisotropic_diffusion imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -bfconvert 1523.0 38.0 ip_convertimage Convert image To update https://github.com/bmcv Imaging, Convert Formats bfconvert imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ 6.7.0+galaxy2 bftools 6.7.0 (0/1) (1/1) (1/1) -binary2labelimage 1273.0 34.0 ip_binary_to_labelimage Binary 2 label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ 0.5 scikit-image (0/1) (1/1) (1/1) -binaryimage2points 29.0 ip_binaryimage_to_points Binary Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ 0.1-2 numpy (0/1) (0/1) (1/1) -bioformats2raw 9.0 bf2raw Convert image to OME-Zarr To update https://github.com/Euro-BioImaging Imaging, Convert Formats bioformats2raw imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw 0.7.0 (0/1) (0/1) (1/1) -color-deconvolution ip_color_deconvolution Color-deconvolution methods galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ 0.8-2 scikit-image (0/1) (0/1) (1/1) -concat_channels 78.0 3.0 ip_concat_channels Concatenate images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -coordinates_of_roi 16546.0 8.0 ip_coordinates_of_roi Coordinates of ROI galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging coordinates_of_roi imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ 0.0.4-2 scikit-image (0/1) (0/1) (1/1) -count_objects 272.0 25.0 ip_count_objects Count Objects galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging count_objects imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ 0.0.5-2 scikit-image (0/1) (1/1) (1/1) -curl_post 440.0 27.0 curl_post Send file via cURL POST To update https://github.com/bmcv Data Export, Web Services curl_post imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post 0.0.2 curl (0/1) (0/1) (1/1) -curve_fitting 12.0 1.0 ip_curve_fitting Polynomial curve fitting to data points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging curve_fitting imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ 0.0.3-2 numpy (0/1) (0/1) (1/1) -detection_viz 46.0 2.0 ip_detection_viz Detection Visualization galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ 0.3-2 scikit-image (0/1) (0/1) (1/1) -image_info 621.0 41.0 ip_imageinfo Extracts image metadata To update https://github.com/bmcv Imaging image_info imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ 5.7.1 bftools 6.7.0 (0/1) (1/1) (1/1) -image_registration_affine 12.0 2.0 ip_image_registration Intensity-based Image Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging image_registration_affine imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ 0.0.3-2 scikit-image (0/1) (0/1) (1/1) -imagecoordinates_flipaxis 21825.0 7.0 imagecoordinates_flipaxis Flip coordinate axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1-2 pandas (0/1) (0/1) (1/1) -labelimage2points 36.0 ip_labelimage_to_points Label Image to Points galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -landmark_registration 857.0 9.0 ip_landmark_registration Landmark Registration galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging landmark_registration imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ 0.1.0-2 scikit-image (1/1) (0/1) (1/1) -mahotas-features ip_mahotas_features Compute image features using mahotas. To update https://github.com/luispedro/mahotas Imaging mahotas_features imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ 0.7-2 mahotas (0/1) (0/1) (1/1) -mergeneighboursinlabelimage 25.0 ip_merge_neighbours_in_label Merge Neighbours in Label Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage 0.3-2 scikit-image (0/1) (0/1) (1/1) -overlay_images 60.0 21.0 ip_overlay_images Overlay two images galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging overlay_images imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ 0.0.4 scikit-image (0/1) (0/1) (1/1) -permutate_axis 42.0 ip_permutate_axis Permutates axes galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -points2binaryimage 41.0 2.0 ip_points_to_binaryimage Points to Binary Image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ 0.2-1 scikit-image (0/1) (0/1) (1/1) -points2labelimage 66.0 ip_points_to_label Points to label image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ 0.3-2 numpy (0/1) (0/1) (1/1) -points_association_nn 29.0 2.0 ip_points_association_nn Association of points in consecutive frames galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging points_association_nn imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ 0.0.3-2 numpy (0/1) (0/1) (1/1) -projective_transformation 44.0 1.0 ip_projective_transformation Projective transformation galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 0.1.2-2 scikit-image (0/1) (0/1) (1/1) -projective_transformation_points 21208.0 9.0 ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging projective_transformation_points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ 0.1.1-2 scikit-image (0/1) (0/1) (1/1) -rfove 7.0 rfove Perform segmentation region-based fitting of overlapping ellipses rfove RFOVE RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. Image analysis Cell biology, Biomedical science, Imaging To update https://sites.google.com/site/costaspanagiotakis/research/cs Imaging rfove imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ 2023.11.12 (0/1) (0/1) (1/1) -scale_image 615.0 9.0 ip_scale_image Scale image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ 0.4-2 pillow (0/1) (0/1) (1/1) -segmetrics 3.0 2.0 ip_segmetrics Image segmentation and object detection performance measures segmetrics SegMetrics Image segmentation and object detection performance measures Image analysis Up-to-date https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ 1.4 segmetrics 1.4 (0/1) (0/1) (1/1) -slice_image 102.0 ip_slice_image Slice image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3-2 scikit-image (0/1) (0/1) (1/1) -split_labelmap 42.0 ip_split_labelmap Split Labelmaps galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2-2 scikit-image (0/1) (0/1) (1/1) -spot_detection_2d 16.0 3.0 ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ 0.0.3-2 imageio (0/1) (0/1) (1/1) -superdsm 16.0 2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.1.3 (0/1) (0/1) (1/1) -unzip 5370.0 508.0 unzip Unzip file To update https://github.com/bmcv Convert Formats unzip imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ 6.0 unzip (0/1) (1/1) (1/1) -visceral-evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 (0/1) (0/1) (1/1) -wsi_extract_top_view 38.0 ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ 0.2-2 scikit-image (0/1) (0/1) (1/1) +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests (0/3) (0/3) (3/3) (0/3) +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 (0/1) (0/1) (1/1) (0/1) +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) (0/1) +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) (1/1) +apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 (1/1) (0/1) (1/1) (0/1) +apollo create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism Access an Apollo instance from Galaxy To update https://github.com/galaxy-genome-annotation/python-apollo Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo apollo 4.2.13 (0/9) (0/9) (9/9) (0/9) +askomics askomics_integrate Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ To update https://github.com/askomics/ Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics askocli 0.5 (0/1) (0/1) (0/1) (0/1) +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 (0/1) (0/1) (0/1) (0/1) +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl (0/1) (0/1) (0/1) (0/1) +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 1.0.0 bamclipper 1.0.0 (0/1) (0/1) (0/1) (0/1) +baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 (0/2) (0/2) (0/2) (2/2) +batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers batched_lastz richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1.04.22 lastz 1.04.22 (1/1) (0/1) (0/1) (0/1) +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel 2.4.0 bio_hansel 2.6.1 (0/1) (0/1) (0/1) (0/1) +biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter 0.2.0 pandas (0/1) (0/1) (0/1) (0/1) +blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) (0/1) +braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) (0/1) +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 (0/1) (1/1) (1/1) (1/1) +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 1.3.0 perl-getopt-long 2.54 (0/1) (1/1) (0/1) (1/1) +camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1.48.0 r-snow 0.4_1 (1/2) (2/2) (2/2) (2/2) +chado analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado To update https://github.com/galaxy-genome-annotation/python-chado Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado python-chado 2.3.9 (0/26) (0/26) (0/26) (0/26) +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 5.1.0 gawk (1/1) (1/1) (1/1) (1/1) +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON 0.1 (0/1) (0/1) (0/1) (0/1) +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 1.0 perl-getopt-long 2.54 (0/1) (0/1) (0/1) (0/1) +combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection 0.1 (0/1) (0/1) (0/1) (0/1) +concat_paired concat_fastqs Concatenate paired datasets To update https://github.com/phac-nml/concat Text Manipulation concat_paired nml https://github.com/phac-nml/concat https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired 0.2 (0/1) (0/1) (0/1) (0/1) +correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis To update http://workflow4metabolomics.org Metabolomics correlation_analysis workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 1.0.1+galaxy0 r-batch 1.1_4 (0/1) (0/1) (0/1) (1/1) +cryptogenotyper 8518.0 16.0 CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. Up-to-date https://github.com/phac-nml/CryptoGenotyper Sequence Analysis cryptogenotyper nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 1.0 cryptogenotyper 1.0 (0/1) (0/1) (1/1) (0/1) +csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files To update https://bioinf.shenwei.me/csvtk/ Text Manipulation csvtk nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0.20.0 csvtk 0.30.0 (0/20) (0/20) (0/20) (1/20) +ectyper 9907.0 53.0 ectyper EC-Typer - in silico serotyping of Escherichia coli species Up-to-date https://github.com/phac-nml/ecoli_serotyping Sequence Analysis ectyper nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 1.0.0 ectyper 1.0.0 (0/1) (0/1) (1/1) (0/1) +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) (7/7) +export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX (0/1) (0/1) (0/1) (0/1) +fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +fasta_extract 10.0 fa-extract-sequence extract single fasta from multiple fasta file To update https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract Sequence Analysis fasta_extract nml https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 1.2 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0.1.0 feht 1.1.0 (0/1) (0/1) (0/1) (0/1) +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 1.0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) (1/1) +gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs To update https://github.com/p2m2/p2m2tools Metabolomics gcms2isocor workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0.2.1 (0/1) (0/1) (0/1) (0/1) +gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +genenotebook genenotebook_build Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io Up-to-date https://genenotebook.github.io Web Services gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook 0.4.15 genoboo 0.4.15 (0/1) (0/1) (1/1) (1/1) +genform 68.0 genform genform: generation of molecular formulas by high-resolution MS and MS/MS data To update https://sourceforge.net/projects/genform/ Metabolomics genform workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform genform r8 (0/1) (0/1) (1/1) (0/1) +get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python (0/1) (0/1) (0/1) (0/1) +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0.1.4.1 srst2 0.2.0 (0/1) (0/1) (0/1) (0/1) +gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 1.1.0 gnali 1.1.0 (0/1) (0/1) (0/1) (0/1) +gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python (0/1) (0/1) (1/1) (0/1) +hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) (0/1) +hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) (0/1) +helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 (0/1) (0/1) (1/1) (1/1) +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace 1.0.1 hivtrace 1.5.0 (0/1) (0/1) (0/1) (0/1) +influx_data_manager influx_data_manager Handling influx_si data inputs in Galaxy workflows Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ Metabolomics influx_si_data_manager workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager 1.0.2 influx-si-data-manager 1.0.2 (0/1) (0/1) (0/1) (1/1) +influx_si influx_si metabolic flux estimation based on [in]stationary labeling To update https://github.com/sgsokol/influx Metabolomics influx_si workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si 7.0.1 influx_si 7.0.4 (0/1) (0/1) (0/1) (1/1) +ipo ipo4retgroup, ipo4xcmsSet [W4M][LC-MS] IPO To update https://github.com/rietho/IPO Metabolomics ipo lecorguille https://github.com/rietho/IPO https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo 1.10.0 bioconductor-ipo 1.28.0 (0/2) (0/2) (0/2) (0/2) +isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) (1/1) +jbrowse 18229.0 2346.0 jbrowse_to_container A tool allowing to export a JBrowse dataset into a JBrowse docker container To update https://jbrowse.org Web Services jbrowse_to_container gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse python (0/1) (0/1) (0/1) (0/1) +kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive 0.3.0 kaptive 3.0.0b1 (0/1) (0/1) (0/1) (0/1) +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) +kat_sect kat_@EXECUTABLE@ SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. To update kat_sect nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect 2.3 kat 2.4.2 (0/1) (0/1) (0/1) (0/1) +kmd_hmdb_data_plot kmd_hmdb_data_plot retrieves data from KMD HMDB API and produce plot and csv file To update https://github.com/workflow4metabolomics/tools-metabolomics Metabolomics kmd_hmdb_data_plot workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot 1.0.0 python (0/1) (0/1) (0/1) (0/1) +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) (0/1) +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) (0/1) +mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 (0/1) (0/1) (0/1) (0/1) +meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 (0/1) (0/1) (0/1) (0/1) +miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) (1/1) +miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl (0/1) (0/1) (0/1) (0/1) +mixmodel4repeated_measures 47.0 2.0 mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model To update http://workflow4metabolomics.org Metabolomics mixmodel4repeated_measures workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 3.1.0 r-lme4 (0/1) (0/1) (0/1) (1/1) +mob_suite 89021.0 322.0 mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies To update https://github.com/phac-nml/mob-suite Sequence Analysis mob_suite nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 3.0.3 mob_suite 3.1.9 (0/2) (2/2) (2/2) (2/2) +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 1.0.2 mrbayes 3.2.7 (0/1) (0/1) (0/1) (0/1) +ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 2.2.1 r-base (0/1) (0/1) (0/1) (1/1) +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0.1.4.1 r-base (0/1) (0/1) (0/1) (0/1) +ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) +nmr_annotation 47.0 3.0 NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 3.0.0 r-batch 1.1_4 (0/1) (0/1) (1/1) (1/1) +nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 2.0.0 r-batch 1.1_4 (0/1) (0/1) (0/1) (1/1) +nmr_preprocessing 140.0 4.0 NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing r-batch 1.1_4 (0/2) (2/2) (2/2) (2/2) +normalization 133.0 13.0 normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data To update http://workflow4metabolomics.org Metabolomics normalization marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 1.0.7 r-batch 1.1_4 (0/1) (1/1) (1/1) (1/1) +openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +pangolin 7276.0 259.0 pangolin Phylogenetic Assignment of Named Global Outbreak LINeages To update https://github.com/hCoV-2019/pangolin Sequence Analysis pangolin nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1.1.14 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0.1.2 python (0/1) (0/1) (0/1) (0/1) +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 (0/4) (0/4) (0/4) (0/4) +physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes To update physiofit.readthedocs.io Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 3.3.5 physiofit 3.3.6 (0/1) (0/1) (0/1) (1/1) +physiofit_manager physiofit_data_manager Handling of physiofit input files To update https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager Metabolomics physiofit_manager workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 1.0.1 physiofit_data_manager (0/1) (0/1) (0/1) (1/1) +plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0.1.6 r (0/1) (0/1) (0/1) (0/1) +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite (0/1) (0/1) (0/1) (0/1) +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 1.1 spades 3.15.5 (0/1) (0/1) (0/1) (0/1) +plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 (0/1) (0/1) (0/1) (0/1) +pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 1.2.1 pneumocat 1.2.1 (0/1) (0/1) (0/1) (0/1) +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 1.2 python (0/1) (0/1) (0/1) (0/1) +pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 1.0.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0.7.0 quasitools 0.7.0 (0/12) (12/12) (0/12) (12/12) +rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 (0/1) (0/1) (0/1) (0/1) +refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 0.1.2 refseq_masher 0.1.2 (0/2) (0/2) (0/2) (2/2) +repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) +replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python (0/1) (0/1) (1/1) (0/1) +rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 (0/1) (0/1) (0/1) (0/1) +segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.2 segalign-full 0.1.2.2 (1/1) (0/1) (0/1) (0/1) +seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 1.0.1 seqtk 1.4 (0/1) (0/1) (0/1) (0/1) +sistr_cmd 2489.0 133.0 sistr_cmd SISTR in silico serotyping tool To update https://github.com/phac-nml/sistr_cmd Sequence Analysis sistr_cmd nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 1.1.1 sistr_cmd 1.1.2 (0/1) (1/1) (1/1) (0/1) +skyline2isocor skyline2isocor Converting skyline output to IsoCor input Up-to-date https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor Metabolomics skyline2isocor workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 1.0.0 skyline2isocor 1.0.0 (0/1) (0/1) (0/1) (1/1) +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0.7.6 smalt 0.7.6 (0/1) (0/1) (0/1) (0/1) +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 (1/1) (0/1) (1/1) (0/1) +spades_header_fixer spades_header_fixer Fixes Spades Fasta ids To update https://github.com/phac-nml/galaxy_tools Fasta Manipulation spades_fasta_header_fixer nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 1.1.2+galaxy1 sed (0/1) (0/1) (0/1) (0/1) +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 (0/1) (0/1) (0/1) (0/1) +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 1.0.1 spolpred (0/1) (0/1) (0/1) (0/1) +srst2 205.0 22.0 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0.3.7 srst2 0.2.0 (0/1) (0/1) (1/1) (0/1) +staramr 12673.0 889.0 staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 (1/1) (1/1) (1/1) (1/1) +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 1.1.0 stringMLST 0.6.3 (0/1) (0/1) (0/1) (0/1) +suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.5.0+q2galaxy.2024.5.0 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.5.0+q2galaxy.2024.5.0 (4/5) (4/5) (4/5) (2/5) +suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.5.0+q2galaxy.2024.5.0 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.5.0+q2galaxy.2024.5.0 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.5.0+q2galaxy.2024.5.0 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.5.0+q2galaxy.2024.5.0 (6/9) (6/9) (6/9) (6/9) +suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.5.0+q2galaxy.2024.5.0 (21/23) (21/23) (21/23) (21/23) +suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.5.0+q2galaxy.2024.5.0 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.5.0+q2galaxy.2024.5.0 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.5.0+q2galaxy.2024.5.0 (10/11) (10/11) (10/11) (10/11) +suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.5.0+q2galaxy.2024.5.0 (17/22) (17/22) (17/22) (17/22) +suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.5.0+q2galaxy.2024.5.0 (3/3) (3/3) (3/3) (3/3) +suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.5.0+q2galaxy.2024.5.0 (11/11) (11/11) (11/11) (11/11) +suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.5.0+q2galaxy.2024.5.0 (3/4) (3/4) (3/4) (3/4) +suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.5.0+q2galaxy.2024.5.0 (12/12) (12/12) (12/12) (12/12) +suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.5.0+q2galaxy.2024.5.0 (6/10) (6/10) (6/10) (6/10) +suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.5.0+q2galaxy.2024.5.0 (1/1) (1/1) (1/1) (1/1) +suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.5.0+q2galaxy.2024.5.0 (0/25) (0/25) (0/25) (0/25) +suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.5.0+q2galaxy.2024.5.0 (15/15) (15/15) (15/15) (15/15) +suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.5.0+q2galaxy.2024.5.0 (4/4) (4/4) (4/4) (4/4) +suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 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+ "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "ToolShed categories": [ + "Assembly", + "Fasta Manipulation", + "Text Manipulation" + ], + "ToolShed id": "seq_primer_clip", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "Galaxy wrapper version": "0.0.18", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5" + }, + { + "Galaxy wrapper id": "seq_rename", + "Galaxy tool ids": [ + "seq_rename" + ], + "Description": "Rename sequences with ID mapping from a tabular file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "seq_rename", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "Galaxy wrapper version": "0.0.10", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5" + }, + { + "Galaxy wrapper id": "seq_select_by_id", + "Galaxy tool ids": [ + "seq_select_by_id" + ], + "Description": "Select sequences by ID", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "seq_select_by_id", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "Galaxy wrapper version": "0.0.15", + "Conda id": "biopython", + "Conda version": "1.70" + }, + { + "Galaxy wrapper id": "venn_list", + "Galaxy tool ids": [ + "venn_list" + ], + "Description": "Draw Venn Diagram (PDF) from lists, FASTA files, etc", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "ToolShed categories": [ + "Graphics", + "Sequence Analysis", + "Visualization" + ], + "ToolShed id": "venn_list", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "Galaxy wrapper version": "0.1.2", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5" + } +] \ No newline at end of file diff --git a/results/repositories02.list_tools.tsv b/results/repositories02.list_tools.tsv index 2331484e..9d2f5e93 100644 --- a/results/repositories02.list_tools.tsv +++ b/results/repositories02.list_tools.tsv @@ -1,331 +1,337 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu -add_value 33763.0 356.0 addValue Add a value as a new column. To update Text Manipulation add_value devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value 1.0.1 perl (1/1) (1/1) (1/1) -annotation_profiler 2.0 Annotation_Profiler_0 Profile Annotations for a set of genomic intervals To update Genomic Interval Operations annotation_profiler devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler 1.0.0 bx-python 0.10.0 (1/1) (0/1) (1/1) -best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) -blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) -blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) -bowtie_wrappers 22988.0 506.0 bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 (0/1) (1/1) (1/1) -canonical_correlation_analysis 72.0 10.0 cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis 1.0.0 R (0/1) (0/1) (1/1) -categorize_elements_satisfying_criteria 40.0 1.0 categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria 1.0.0 (0/1) (1/1) (1/1) -ccat 165.0 15.0 peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat 0.0.2 ccat 3.0 (0/1) (0/1) (1/1) -cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) -change_case ChangeCase Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case 1.0.1 perl (1/1) (1/1) (1/1) -compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) -compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) -compute_q_values 35.0 compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values 1.0.1 R (0/1) (0/1) (0/1) -condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters 1.0.0 (1/1) (1/1) (0/1) -convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters 1.0.1 python (1/1) (1/1) (1/1) -convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc 1.0.0 (0/1) (0/1) (0/1) -correlation 809.0 47.0 cor2 Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation 1.0.0 rpy (0/1) (1/1) (1/1) -count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) -ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) -cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) -cummerbund_to_tabular 1204.0 13.0 cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular 1.0.1 (1/1) (0/1) (1/1) -cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns 1.0.2 (1/1) (1/1) (1/1) -delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) -dgidb_annotator 231.0 30.0 dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator 0.1 (0/1) (0/1) (1/1) -divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) -draw_stacked_barplots 173.0 12.0 draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots 1.0.0 R (0/1) (1/1) (1/1) -dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) -dwt_var_perfeature 36.0 dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature 1.0.2 r-bitops (1/1) (1/1) (1/1) -express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) -fasta_compute_length 7758.0 380.0 fasta_compute_length Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.3 python (1/1) (1/1) (1/1) -fasta_concatenate_by_species 35793.0 88.0 fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -fasta_filter_by_length 48649.0 350.0 fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length 1.2 python (1/1) (1/1) (1/1) -fasta_to_tabular 105841.0 622.0 fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular 1.1.1 python (1/1) (1/1) (1/1) -fastq_trimmer_by_quality 5485.0 459.0 fastq_quality_trimmer FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual 1.0.0 (0/1) (0/1) (0/1) -featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter 2.0.0 bx-python 0.10.0 (1/1) (0/1) (1/1) -filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) -generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) -getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) -gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) -hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) -histogram 2367.0 94.0 histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 1.0.4 rpy2 2.7.8 (1/1) (1/1) (1/1) -indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) -kernel_canonical_correlation_analysis 69.0 2.0 kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis 1.0.0 rpy (1/1) (0/1) (1/1) -kernel_principal_component_analysis 155.0 13.0 kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis 1.0.0 rpy (1/1) (0/1) (1/1) -lastz_paired_reads 9.0 1.0 lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 (0/1) (1/1) (1/1) -lda_analysis 148.0 18.0 lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis 1.0.1 R (1/1) (0/1) (1/1) -linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression 1.0.1 R (1/1) (0/1) (0/1) -logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) -maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 1.0.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) -megablast_xml_parser 338.0 36.0 megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser 1.0.1 python (1/1) (0/1) (1/1) -merge_cols 21906.0 536.0 mergeCols1 Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols 1.0.3 python (1/1) (1/1) (1/1) -microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) -microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) -microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability 1.1.0 bx-python 0.10.0 (1/1) (0/1) (0/1) -mine 11.0 2.0 maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine 0.0.1 MINE (1/1) (0/1) (1/1) -multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) -mutate_snp_codon 47.0 mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon 1.0.0 (1/1) (0/1) (1/1) -partialr_square partialRsq Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square 1.0.0 R (1/1) (0/1) (0/1) -pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation 1.0.0 (0/1) (0/1) (0/1) -pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp 1.0.0 (0/1) (0/1) (0/1) -pileup_interval 632.0 15.0 pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval 1.0.3 bx-python 0.10.0 (1/1) (1/1) (1/1) -pileup_parser 3158.0 169.0 pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser 1.0.2 perl (1/1) (1/1) (1/1) -plot_from_lda 73.0 9.0 plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda 1.0.1 R (1/1) (0/1) (1/1) -principal_component_analysis 9986.0 88.0 pca1 Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis 1.0.2 rpy (1/1) (0/1) (1/1) -quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 1.0.1 bx-python 0.10.0 (0/1) (0/1) (0/1) -rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) -remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning 1.0.0 (1/1) (1/1) (1/1) -rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) -rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) -sam2interval 1189.0 20.0 sam2interval Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval 1.0.2 python (1/1) (1/1) (1/1) -sam_bitwise_flag_filter 261.0 1.0 sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter 1.0.1 python (1/1) (1/1) (0/1) -scatterplot 1637.0 61.0 scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot 1.0.3 numpy (1/1) (0/1) (1/1) -short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) -short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) -short_reads_trim_seq 220.0 21.0 trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq 1.0.0 (1/1) (0/1) (1/1) -show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning 1.0.0 (1/1) (1/1) (1/1) -show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail 1.0.0 (1/1) (1/1) (1/1) -sicer 374.0 5.0 peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer 1.1 SICER 1.1 (1/1) (1/1) (1/1) -split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads 1.0.0 (0/1) (0/1) (0/1) -substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) -substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) -t_test_two_samples 210.0 6.0 t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples 1.0.1 R (1/1) (1/1) (1/1) -table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar 0.2 annovar (0/1) (0/1) (0/1) -tabular_to_fasta 319234.0 601.0 tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta 1.1.1 python (1/1) (1/1) (1/1) -tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat 1.5.0 samtools 1.19.2 (0/1) (0/1) (0/1) -tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 2.1.1 bowtie2 2.5.3 (1/1) (1/1) (1/1) -tophat_fusion_post 216.0 15.0 tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post 0.1 blast+ (0/1) (1/1) (1/1) -trimmer 6058.0 188.0 trimmer Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer 0.0.1 (1/1) (1/1) (1/1) -ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) -varscan_version_2 5191.0 246.0 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 2.4.2 varscan 2.4.6 (1/1) (1/1) (1/1) -vcf2pgsnp 206.0 15.0 vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp 1.0.0 (1/1) (0/1) (1/1) -vcf_annotate 1.0 vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate 1.0.0 (0/1) (0/1) (0/1) -vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract 1.0.0 (0/1) (0/1) (0/1) -vcf_filter 388.0 63.0 vcf_filter Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter 1.0.0 (0/1) (0/1) (1/1) -vcf_intersect 19.0 vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect 1.0.0 (0/1) (0/1) (0/1) -weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) -windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) -xy_plot 5890.0 344.0 XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot 1.0.2 r-base (1/1) (1/1) (1/1) -basecoverage 307.0 2.0 gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -cluster 791.0 1.0 gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -complement 233.0 1.0 gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -concat 564897.0 309.0 gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat 1.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -coverage 1489.0 17.0 gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -flanking_features 671.0 20.0 flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features 4.0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -get_flanks 324380.0 555.0 get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -intersect 347919.0 1003.0 gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -join 329478.0 284.0 gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -merge 563676.0 193.0 gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -subtract 564149.0 182.0 gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract 1.0.0 bx-python 0.10.0 (1/1) (1/1) (1/1) -subtract_query 1014.0 55.0 subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query 0.1 bx-python 0.10.0 (1/1) (1/1) (1/1) -tables_arithmetic_operations 2207.0 14.0 tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl (0/1) (0/1) (1/1) -hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) -hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) -snpfreq 37.0 7.0 hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq 1.0.1 R (1/1) (1/1) (1/1) -find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) -kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk (1/1) (1/1) (1/1) -lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) -poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 (0/1) (1/1) (1/1) -t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) -vcftools_annotate 171.0 24.0 vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate 0.1 echo (1/1) (0/1) (1/1) -vcftools_compare 531.0 34.0 vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 (0/1) (0/1) (1/1) -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.19.2 (0/1) (0/1) (0/1) -vcftools_isec 498.0 35.0 vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 (0/1) (1/1) (1/1) -vcftools_merge 953.0 68.0 vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 (0/1) (1/1) (1/1) -vcftools_slice 411.0 24.0 vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice 0.1 echo (1/1) (0/1) (1/1) -vcftools_subset 137.0 17.0 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) -10x_bamtofastq 228.0 46.0 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) -AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) -Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) -PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) -agat 481.0 42.0 agat GTF/GFF analysis toolkit agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics Up-to-date https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.2.0 (0/1) (0/1) (1/1) -antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 (1/1) (1/1) (1/1) -atactk_trim_adapters 257.0 26.0 atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters 0.1.6 atactk 0.1.9 (0/1) (0/1) (1/1) -augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) -bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) -barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.0 (0/1) (0/1) (0/1) -bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools (0/1) (0/1) (1/1) -biomodelsML biomodels_biomd0000001066, biomodels_BIOMD0000001076 Random Forest model to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts To update https://www.ebi.ac.uk/biomodels/BIOMD0000001066 Machine Learning biomodels_biomd0000001066 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1 (0/2) (0/2) (1/2) -bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) -bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (0/4) (4/4) -blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) -blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) -canu 13021.0 533.0 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 (0/1) (1/1) (1/1) -cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools (0/23) (23/23) (23/23) -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.6 (0/1) (0/1) (1/1) -chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) -circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann Combine Metaphlan and HUMAnN """This tool combine MetaPhlAn outputs and HUMANnN outputs."" - Galaxy tool wrapper" Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 0.3.0 python (0/1) (0/1) (1/1) -compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs Compare HUMAnN2 outputs """This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples."" - Galaxy tool wrapper" Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) -cpat 134.0 21.0 cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.4 cpat 3.0.4 (1/1) (1/1) (1/1) -crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) -diff 235.0 30.0 diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils (0/1) (0/1) (1/1) -diffbind 6264.0 250.0 Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind (0/1) (0/1) (0/1) -edta 484.0 58.0 edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta edta 2.2.0 (0/1) (0/1) (1/1) -epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 (0/1) (0/1) (1/1) -fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) -file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) -find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening 0.3 biopython 1.70 (1/1) (0/1) (1/1) -flye 20904.0 1499.0 flye Assembly of long and error-prone reads. To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.1 flye 2.9.3 (1/1) (1/1) (1/1) -footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) -format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ 1.0.0+galaxy1 (0/1) (0/1) (1/1) -format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output Format metaphlan2 output """This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)."" - Galaxy tool wrapper" Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 (0/1) (0/1) (1/1) -gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) -glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) -gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) -graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 (0/1) (0/1) (0/1) -graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) -graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) -hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 0.99 hclust2 1.0.0 (0/1) (0/1) (0/1) -hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 (7/7) (0/7) (7/7) -hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler Up-to-date https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.8 (1/1) (1/1) (1/1) -homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) -illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) -bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools 0.1.0 wget (0/1) (0/1) (1/1) -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.40 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) -imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) -instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) -iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) -itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) -jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 (0/1) (0/1) (0/1) -labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) -lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data To update Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/mourisl/Lighter 1.0 lighter 1.1.2 (0/1) (0/1) (1/1) -mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.508 mafft 7.520 (2/2) (2/2) (2/2) -mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ 0.9 (0/1) (0/1) (1/1) -mcl 29.0 10.0 mcl_clustering Markov Cluster Algorithm To update http://micans.org/mcl/ Sequence Analysis, Metagenomics mcl bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mcl 14.137 mcl 22.282 (0/1) (0/1) (0/1) -methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) -methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) -methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 (0/1) (0/1) (0/1) -metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) -miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) -minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) -minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) -mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (0/1) (1/1) -molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) -music_deconvolution 530.0 67.0 music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ 0.1.1 music-deconvolution 0.1.1 (5/5) (5/5) (4/5) -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 (0/4) (4/4) (4/4) -netboxr 11.0 5.0 netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening 1.6.0 bioconductor-netboxr 1.9.0 (0/1) (0/1) (1/1) -nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) -nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) -numeric_clustering 486.0 numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda (0/1) (0/1) (0/1) -openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (0/140) (34/140) (135/140) -pandas_rolling_window 269.0 7.0 pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy (1/1) (0/1) (1/1) -peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) -perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf (0/1) (0/1) (0/1) -pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) -pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools postgresql (0/3) (0/3) (0/3) -pharmcat 82.0 14.0 pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat (1/1) (0/1) (1/1) -piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) -platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) -plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas (1/1) (1/1) (1/1) -plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) -plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) -protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) -protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) -improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) -racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon The Possibility to Use Oxford Nanopore Technology | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: https://github.com/isovic/racon| Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step | Consensus module for raw de novo DNA assembly of long uncorrected reads Genome assembly, Mapping assembly, Sequence trimming Whole genome sequencing, Sequence assembly, Plant biology Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) -repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) -replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn 0.2 (1/1) (1/1) (1/1) -rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 (0/1) (0/1) (0/1) -antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) -aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) -blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) -cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy0 perl (0/1) (0/1) (1/1) -cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) -cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) -compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ 1.0 compalignp 1.0 (0/1) (0/1) (1/1) -coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) -dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) -dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 (0/1) (0/1) (1/1) -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 (0/1) (0/1) (0/1) -dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) -exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) -graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) -htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) -infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs Up-to-date http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal 1.1.4 infernal 1.1.4 (0/6) (6/6) (6/6) -inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) -intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) -kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) -locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) -mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) -mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 (0/1) (0/1) (1/1) -nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) -paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) -pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) -rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) -rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) -rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) -reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (0/1) -remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) -ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) -rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) -rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) -rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) -rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) -rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) -rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) -rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) -selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) -sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) -sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) -targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) -trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) -vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) -sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) -salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.2 (2/3) (1/3) (3/3) -sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_slice, sambamba_sort, sambamba_view, sambamba_depth SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba sambamba 1.0 (0/7) (0/7) (0/7) -sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed (0/1) (0/1) (0/1) -segemehl 1276.0 30.0 segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 (0/1) (0/1) (1/1) -sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 (30/33) (14/33) (31/33) -splitfasta 1295.0 96.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 (1/1) (0/1) (1/1) -statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy (0/1) (0/1) (1/1) -stress_ng 47.0 stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng 0.12.04 stress-ng (0/1) (0/1) (0/1) -add_line_to_file 14480.0 193.0 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) -column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 (1/1) (1/1) (1/1) -join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1) -split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1) -split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.1 python (1/1) (1/1) (1/1) -text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 0.1.1 coreutils 8.25 (19/19) (19/19) (19/19) -tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) -tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1) -trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) -uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.4 requests (1/1) (1/1) (1/1) -vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) -wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) -align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) -chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) -clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.19.2 (0/2) (0/2) (0/2) -clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) -count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.19.2 (0/1) (0/1) (0/1) -coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.19.2 (0/1) (0/1) (0/1) -effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.20 effectiveT3 1.0.1 (0/1) (0/1) (0/1) -fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) -mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) -nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) -predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) -protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) -sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) -samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.19.2 (0/1) (0/1) (0/1) -samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.19.2 (1/1) (0/1) (1/1) -samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.19.2 (1/1) (1/1) (1/1) -seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) -seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) -seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) -seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) -seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) -seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) -venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +10x_bamtofastq 228.0 46.0 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) (0/1) +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) (0/2) +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) (0/1) +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +add_line_to_file 14480.0 193.0 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +add_value 33763.0 356.0 addValue Add a value as a new column. To update Text Manipulation add_value devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1.0.1 perl (1/1) (1/1) (1/1) (1/1) +agat 481.0 42.0 agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.4.0 (0/1) (0/1) (1/1) (1/1) +align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +annotation_profiler 2.0 Annotation_Profiler_0 Profile Annotations for a set of genomic intervals To update Genomic Interval Operations annotation_profiler devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler 1.0.0 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) (0/1) +antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 (1/1) (1/1) (1/1) (0/1) +aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) (0/1) +atactk_trim_adapters 257.0 26.0 atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 (0/1) (0/1) (1/1) (0/1) +augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) (1/1) +bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) (0/1) +barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +basecoverage 307.0 2.0 gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) (1/1) +bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) +bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools (0/1) (0/1) (1/1) (0/1) +biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 (0/2) (0/2) (2/2) (0/2) +bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) (0/1) +bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (4/4) (4/4) (4/4) +blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) (0/1) +blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) (0/1) +blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) (0/1) +blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) (0/1) +blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) (0/1) +bowtie_wrappers 22988.0 506.0 bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 (0/1) (1/1) (1/1) (0/1) +canonical_correlation_analysis 72.0 10.0 cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 1.0.0 R (0/1) (0/1) (1/1) (1/1) +canu 13021.0 533.0 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 (0/1) (1/1) (1/1) (1/1) +categorize_elements_satisfying_criteria 40.0 1.0 categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 1.0.0 (0/1) (1/1) (1/1) (0/1) +ccat 165.0 15.0 peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0.0.2 ccat 3.0 (0/1) (0/1) (1/1) (0/1) +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 (1/1) (0/1) (0/1) (0/1) +cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.8 cellpose (0/1) (0/1) (1/1) (0/1) +cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) +change_case ChangeCase Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1.0.1 perl (1/1) (1/1) (1/1) (1/1) +chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) (0/1) +chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) (0/1) +clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.20 (0/2) (0/2) (0/2) (0/2) +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) (0/1) +cluster 791.0 1.0 gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl (0/1) (0/1) (1/1) (0/1) +cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) (0/4) +cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) (0/1) +column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 (1/1) (1/1) (1/1) (1/1) +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python (0/1) (0/1) (1/1) (0/1) +compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 (0/1) (0/1) (1/1) (0/1) +compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) (0/1) +complement 233.0 1.0 gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +compute_motif_frequencies_for_all_motifs 94.0 2.0 compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 1.0.0 (0/1) (1/1) (1/1) (0/1) +compute_motifs_frequency 65.0 compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 1.0.0 (0/1) (1/1) (1/1) (0/1) +compute_q_values 35.0 compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 1.0.1 R (0/1) (0/1) (0/1) (0/1) +concat 564897.0 309.0 gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1.0.0 (1/1) (1/1) (0/1) (0/1) +convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1.0.1 python (1/1) (1/1) (1/1) (1/1) +convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 1.0.0 (0/1) (0/1) (0/1) (0/1) +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) (0/1) +correlation 809.0 47.0 cor2 Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 1.0.0 rpy (0/1) (1/1) (1/1) (1/1) +count_gff_features 271.0 49.0 count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 0.2 galaxy-ops 1.1.0 (1/1) (1/1) (1/1) (1/1) +count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +coverage 1489.0 17.0 gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +cpat 134.0 21.0 cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 (1/1) (1/1) (1/1) (1/1) +crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) (0/1) +ctd_batch 203.0 13.0 ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 1.0.0 (0/1) (0/1) (1/1) (0/1) +cummerbund 1782.0 31.0 cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 2.16.0 fonts-conda-ecosystem (1/1) (1/1) (1/1) (0/1) +cummerbund_to_tabular 1204.0 13.0 cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1.0.1 (1/1) (0/1) (1/1) (0/1) +cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1.0.2 (1/1) (1/1) (1/1) (1/1) +delete_overlapping_indels 39.0 2.0 delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 1.0.0 (0/1) (0/1) (1/1) (0/1) +dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) (0/1) +dgidb_annotator 231.0 30.0 dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0.1 (0/1) (0/1) (1/1) (0/1) +diff 235.0 30.0 diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils (1/1) (0/1) (1/1) (0/1) +diffbind 6264.0 250.0 Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind (0/1) (0/1) (0/1) (0/1) +divide_pg_snp 31.0 dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1.0.0 (1/1) (0/1) (1/1) (0/1) +dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 (0/1) (0/1) (1/1) (0/1) +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 (0/1) (0/1) (0/1) (0/1) +dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) (0/1) +draw_stacked_barplots 173.0 12.0 draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 1.0.0 R (0/1) (1/1) (1/1) (1/1) +dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 (0/1) (1/1) (0/1) (0/1) +dwt_var_perfeature 36.0 dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature 1.0.2 r-bitops (1/1) (1/1) (1/1) (1/1) +edta 484.0 58.0 edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 (0/1) (0/1) (1/1) (0/1) +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 (0/1) (0/1) (0/1) (0/1) +epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 (0/1) (0/1) (1/1) (0/1) +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) (0/1) +express 325.0 12.0 express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 1.1.1 eXpress 1.5.1 (0/1) (1/1) (1/1) (0/1) +fasta_compute_length 7758.0 380.0 fasta_compute_length Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1.0.3 python (1/1) (1/1) (1/1) (1/1) +fasta_concatenate_by_species 35793.0 88.0 fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fasta_filter_by_length 48649.0 350.0 fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1.2 python (1/1) (1/1) (1/1) (1/1) +fasta_to_tabular 105841.0 622.0 fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1.1.1 python (1/1) (1/1) (1/1) (1/1) +fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) (0/1) +fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_trimmer_by_quality 5485.0 459.0 fastq_quality_trimmer FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 1.0.0 (0/1) (0/1) (0/1) (0/1) +featurecounter 22384.0 6.0 featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 2.0.0 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) (1/1) +filter_transcripts_via_tracking 20.0 1.0 filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 0.1 (1/1) (1/1) (1/1) (1/1) +find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +flanking_features 671.0 20.0 flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 4.0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.4 (1/1) (1/1) (1/1) (1/1) +footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) (0/1) +format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 (0/1) (0/1) (1/1) (0/1) +format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 (0/1) (0/1) (1/1) (0/1) +generate_pc_lda_matrix 119.0 12.0 generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1.0.0 (1/1) (1/1) (1/1) (1/1) +get_flanks 324380.0 555.0 get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) (1/1) +getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1.0.0 numpy (1/1) (0/1) (0/1) (0/1) +gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) (0/1) +gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation gi2taxonomy gi2taxonomy gi2taxonomy The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). Database search, ID mapping Taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) (0/1) +gmaj 11.0 4.0 gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 2.0.1 (1/1) (1/1) (1/1) (1/1) +gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) (0/1) +graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 (0/1) (0/1) (0/1) (0/1) +graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) (0/1) +graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.43 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) (0/2) +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) (0/1) +hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 (0/1) (0/1) (0/1) (0/1) +hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) (0/1) +hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) (0/1) +hictk hictk Convert cooler to juicebox_hic Up-to-date https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0.0.12 hictk 0.0.12 (0/1) (0/1) (1/1) (0/1) +hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 (7/7) (0/7) (7/7) (0/7) +hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler To update https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.9 (1/1) (1/1) (1/1) (1/1) +hisat 228.0 hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 1.0.3 hisat (0/1) (0/1) (0/1) (0/1) +histogram 2367.0 94.0 histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1.0.4 rpy2 2.7.8 (1/1) (1/1) (1/1) (1/1) +homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) (0/1) +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) (0/1) +illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) (0/1) +imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) (0/27) +improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) (0/1) +indels_3way 22.0 indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way 1.0.3 (1/1) (0/1) (1/1) (0/1) +infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 (0/6) (6/6) (6/6) (0/6) +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) (0/1) +instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) (0/1) +intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) (0/1) +intersect 347919.0 1003.0 gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) (0/1) +itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) (0/1) +join 329478.0 284.0 gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1) (1/1) +jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 (0/1) (0/1) (0/1) (0/1) +kernel_canonical_correlation_analysis 69.0 2.0 kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1.0.0 rpy (1/1) (0/1) (1/1) (1/1) +kernel_principal_component_analysis 155.0 13.0 kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1.0.0 rpy (1/1) (0/1) (1/1) (1/1) +kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) (0/1) +kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1.2+galaxy0 gawk (1/1) (1/1) (1/1) (0/1) +labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) (0/1) +lastz_paired_reads 9.0 1.0 lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 (0/1) (1/1) (1/1) (0/1) +lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +lda_analysis 148.0 18.0 lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis 1.0.1 R (1/1) (0/1) (1/1) (1/1) +lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.3 (0/1) (0/1) (1/1) (0/1) +linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression 1.0.1 R (1/1) (0/1) (0/1) (0/1) +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) (0/5) +logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 1.0.1 numpy (0/1) (0/1) (0/1) (0/1) +maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1.0.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.520 mafft 7.525 (2/2) (2/2) (2/2) (2/2) +mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 1.0.0 (0/1) (0/1) (0/1) (0/1) +mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 (0/1) (0/1) (1/1) (0/1) +mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) (0/1) +megablast_xml_parser 338.0 36.0 megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1.0.1 python (1/1) (0/1) (1/1) (0/1) +merge 563676.0 193.0 gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +merge_cols 21906.0 536.0 mergeCols1 Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1.0.3 python (1/1) (1/1) (1/1) (1/1) +methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) (0/8) +methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) (0/1) +methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 (0/1) (0/1) (0/1) (1/1) +metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) (1/1) +mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers To update https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis mgnify_seqprep bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep 1.2 (0/1) (0/1) (0/1) (0/1) +miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) (0/1) +microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 1.0.0 (0/1) (0/1) (0/1) (0/1) +microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level 1.0.0 sputnik (1/1) (0/1) (0/1) (0/1) +microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1.1.0 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) (0/1) +mine 11.0 2.0 maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 0.0.1 MINE (1/1) (0/1) (1/1) (1/1) +minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) (0/1) +mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (1/1) (1/1) (0/1) +molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 (0/1) (0/1) (1/1) (0/1) +multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik (0/1) (0/1) (0/1) (0/1) +mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) (0/1) +music_deconvolution 530.0 67.0 music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 (5/5) (5/5) (4/5) (0/5) +mutate_snp_codon 47.0 mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1.0.0 (1/1) (0/1) (1/1) (0/1) +nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 (0/4) (4/4) (4/4) (4/4) +nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) (0/1) +netboxr 11.0 5.0 netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 (0/1) (0/1) (1/1) (0/1) +nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) (0/1) +nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) (0/1) +nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) (0/1) +numeric_clustering 486.0 numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda (0/1) (0/1) (0/1) (1/1) +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (7/140) (34/140) (135/140) (0/140) +pandas_rolling_window 269.0 7.0 pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy (1/1) (0/1) (1/1) (0/1) +paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) (0/1) +partialr_square partialRsq Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square 1.0.0 R (1/1) (0/1) (0/1) (0/1) +peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) (0/1) +pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation 1.0.0 (0/1) (0/1) (0/1) (0/1) +perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf (0/1) (0/1) (0/1) (0/1) +pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) (1/1) +pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql (0/3) (0/3) (0/3) (0/3) +pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp 1.0.0 (0/1) (0/1) (0/1) (0/1) +pharmcat 82.0 14.0 pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat (1/1) (0/1) (1/1) (0/1) +pileup_interval 632.0 15.0 pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1.0.3 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +pileup_parser 3158.0 169.0 pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1.0.2 perl (1/1) (1/1) (1/1) (1/1) +pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) (0/1) +piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) (0/1) +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) (0/1) +plot_from_lda 73.0 9.0 plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda 1.0.1 R (1/1) (0/1) (1/1) (1/1) +plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.3 galaxy-ml 0.10.0 (1/1) (1/1) (1/1) (0/1) +plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) (0/1) +plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) (0/1) +poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 (0/1) (1/1) (1/1) (0/1) +predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) (0/1) +principal_component_analysis 9986.0 88.0 pca1 Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis 1.0.2 rpy (1/1) (0/1) (1/1) (1/1) +protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) (0/1) +protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) (0/6) +protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 1.0.1 bx-python 0.11.0 (0/1) (0/1) (0/1) (0/1) +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) +racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) (1/1) +rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) +rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) (0/1) +rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1.0.0 R (1/1) (0/1) (0/1) (0/1) +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (1/1) (0/1) +remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1.0.0 (1/1) (1/1) (1/1) (1/1) +remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) (0/1) +repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 (1/1) (1/1) (1/1) (1/1) +rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 (0/1) (0/1) (0/1) (0/1) +ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) (0/3) +rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) (0/1) +rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 1.0.0 rmap 2.1 (0/1) (0/1) (0/1) (0/1) +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) (0/1) +rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) (0/1) +rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) (0/1) +rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) (0/1) +rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) (0/1) +rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) (0/1) +rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) (0/6) +sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) (1/1) +salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) +sam2interval 1189.0 20.0 sam2interval Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1.0.2 python (1/1) (1/1) (1/1) (1/1) +sam_bitwise_flag_filter 261.0 1.0 sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1.0.1 python (1/1) (1/1) (0/1) (1/1) +sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_slice, sambamba_sort, sambamba_view, sambamba_depth SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba sambamba 1.0.1 (0/7) (0/7) (0/7) (0/7) +sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +scatterplot 1637.0 61.0 scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1.0.3 numpy (1/1) (0/1) (1/1) (1/1) +sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed (0/1) (0/1) (0/1) (0/1) +segemehl 1276.0 30.0 segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 (0/1) (0/1) (1/1) (0/1) +selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) (0/1) +seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) (1/1) +seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) (0/1) +short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 1.0.0 rpy (0/1) (0/1) (0/1) (0/1) +short_reads_figure_score 163.0 13.0 quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 1.0.2 fontconfig (0/1) (0/1) (1/1) (0/1) +short_reads_trim_seq 220.0 21.0 trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1.0.0 (1/1) (0/1) (1/1) (0/1) +show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1.0.0 (1/1) (1/1) (1/1) (1/1) +show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1.0.0 (1/1) (1/1) (1/1) (1/1) +sicer 374.0 5.0 peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1.1 SICER 1.1 (1/1) (1/1) (1/1) (1/1) +sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 (30/33) (14/33) (31/33) (16/33) +snpfreq 37.0 7.0 hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1.0.1 R (1/1) (1/1) (1/1) (0/1) +sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) (1/1) +split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1) (1/1) +split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python (1/1) (1/1) (1/1) (1/1) +split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 1.0.0 (0/1) (0/1) (0/1) (0/1) +splitfasta 1295.0 96.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) (0/1) +statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy (0/1) (0/1) (1/1) (0/1) +stress_ng 47.0 stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng (0/1) (0/1) (0/1) (0/1) +substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 1.0.0 (0/1) (0/1) (0/1) (0/1) +substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +subtract 564149.0 182.0 gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1.0.0 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +subtract_query 1014.0 55.0 subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 0.1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +t2ps 457.0 31.0 Draw_phylogram Draw phylogeny t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" Phylogenetic tree visualisation Phylogenomics To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) +t_test_two_samples 210.0 6.0 t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R (1/1) (1/1) (1/1) (1/1) +table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar (0/1) (0/1) (0/1) (0/1) +tables_arithmetic_operations 2207.0 14.0 tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl (0/1) (0/1) (1/1) (1/1) +tabular_to_fasta 319234.0 601.0 tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python (1/1) (1/1) (1/1) (1/1) +tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) +targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) (0/1) +text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 (20/20) (20/20) (20/20) (20/20) +tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) (0/1) +tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. Tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation To update https://github.com/ibe-uw/tiara Metagenomics, Sequence Analysis tiara bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara 1.0.3 tiara (0/1) (0/1) (0/1) (0/1) +tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1) (0/1) +tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.4 (1/1) (1/1) (1/1) (0/1) +tophat_fusion_post 216.0 15.0 tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ (0/1) (1/1) (1/1) (0/1) +trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) +trimmer 6058.0 188.0 trimmer Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 (1/1) (1/1) (1/1) (1/1) +trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) (0/2) +ucsc_custom_track 393.0 45.0 build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python (1/1) (0/1) (1/1) (0/1) +uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.5 requests (1/1) (1/1) (1/1) (0/1) +varscan_version_2 5191.0 246.0 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 2.4.2 varscan 2.4.6 (1/1) (1/1) (1/1) (1/1) +vcf2pgsnp 206.0 15.0 vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1.0.0 (1/1) (0/1) (1/1) (0/1) +vcf_annotate 1.0 vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 1.0.0 (0/1) (0/1) (0/1) (0/1) +vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 1.0.0 (0/1) (0/1) (0/1) (0/1) +vcf_filter 388.0 63.0 vcf_filter Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 1.0.0 (0/1) (0/1) (1/1) (0/1) +vcf_intersect 19.0 vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 1.0.0 (0/1) (0/1) (0/1) (0/1) +vcftools_annotate 171.0 24.0 vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo (1/1) (0/1) (1/1) (1/1) +vcftools_compare 531.0 34.0 vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) +vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +vcftools_isec 498.0 35.0 vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 (0/1) (1/1) (1/1) (0/1) +vcftools_merge 953.0 68.0 vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 (0/1) (1/1) (1/1) (0/1) +vcftools_slice 411.0 24.0 vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo (1/1) (0/1) (1/1) (1/1) +vcftools_subset 137.0 17.0 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) +venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) (1/1) +vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) (0/23) +vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) (0/1) +weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 (1/1) (0/1) (0/1) (0/1) +whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. To update https://github.com/bgruening/galaxytools/tree/master/tools/whisper Machine Learning whisper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 (0/1) (0/1) (1/1) (0/1) +windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1.0.1 bx-python 0.11.0 (1/1) (0/1) (0/1) (0/1) +woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 (0/1) (0/1) (1/1) (0/1) +wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) (1/1) +xy_plot 5890.0 344.0 XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1.0.2 r-base (1/1) (1/1) (1/1) (1/1) diff --git a/results/repositories03.list_tools.json b/results/repositories03.list_tools.json new file mode 100644 index 00000000..a50f283b --- /dev/null +++ b/results/repositories03.list_tools.json @@ -0,0 +1,19586 @@ +[ + { + "Galaxy wrapper id": "TrimNs", + "Galaxy tool ids": [ + "trimns" + ], + "Description": "TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "trimns", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs", + "Galaxy wrapper version": "0.1.0", + "Conda id": "trimns_vgp", + "Conda version": "1.0" + }, + { + "Galaxy wrapper id": "abricate", + "Galaxy tool ids": [ + "abricate", + "abricate_list", + "abricate_summary" + ], + "Description": "Mass screening of contigs for antiobiotic resistance genes", + "bio.tool id": "ABRicate", + "bio.tool ids": [ + "ABRicate" + ], + "biii": null, + "bio.tool name": "ABRicate", + "bio.tool description": "Mass screening of contigs for antimicrobial resistance or virulence genes.", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Genomics", + "Microbiology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/abricate", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "abricate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate", + "Galaxy wrapper version": "1.0.1", + "Conda id": "abricate", + "Conda version": "1.0.1" + }, + { + "Galaxy wrapper id": "abritamr", + "Galaxy tool ids": [ + "abritamr" + ], + "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", + "bio.tool id": "abritamr", + "bio.tool ids": [ + "abritamr" + ], + "biii": null, + "bio.tool name": "abriTAMR", + "bio.tool description": "an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Microbiology", + "Public health and epidemiology", + "Infectious disease" + ], + "Status": "To update", + "Source": "https://zenodo.org/record/7370628", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "abritamr", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", + "Galaxy wrapper version": "1.0.14", + "Conda id": "abritamr", + "Conda version": "1.0.17" + }, + { + "Galaxy wrapper id": "abyss", + "Galaxy tool ids": [ + "abyss-pe" + ], + "Description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", + "bio.tool id": "abyss", + "bio.tool ids": [ + "abyss" + ], + "biii": null, + "bio.tool name": "ABySS", + "bio.tool description": "De novo genome sequence assembler using short reads.", + "EDAM operation": [ + "Genome assembly", + "De-novo assembly", + "Scaffolding" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "http://www.bcgsc.ca/platform/bioinfo/software/abyss", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "abyss", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", + "Galaxy wrapper version": "2.3.7", + "Conda id": "abyss", + "Conda version": "2.3.7" + }, + { + "Galaxy wrapper id": "adapter_removal", + "Galaxy tool ids": [ + "adapter_removal" + ], + "Description": "Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.", + "bio.tool id": "adapterremoval", + "bio.tool ids": [ + "adapterremoval" + ], + "biii": null, + "bio.tool name": "AdapterRemoval", + "bio.tool description": "AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.", + "EDAM operation": [ + "Sequence trimming", + "Sequence merging", + "Primer removal" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/MikkelSchubert/adapterremoval", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "adapter_removal", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal", + "Galaxy wrapper version": "2.3.3", + "Conda id": "adapterremoval", + "Conda version": "2.3.3" + }, + { + "Galaxy wrapper id": "add_input_name_as_column", + "Galaxy tool ids": [ + "addName" + ], + "Description": "Add input name as column on an existing tabular file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "add_input_name_as_column", + "Galaxy wrapper owner": "mvdbeek", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null + }, + { + "Galaxy wrapper id": "aegean", + "Galaxy tool ids": [ + "aegean_canongff3", + "aegean_gaeval", + "aegean_locuspocus", + "aegean_parseval" + ], + "Description": "AEGeAn toolkit wrappers", + "bio.tool id": "gaeval", + "bio.tool ids": [ + "gaeval" + ], + "biii": null, + "bio.tool name": "GAEVAL", + "bio.tool description": "Gene Annotation EVAluation.", + "EDAM operation": [ + "Sequence annotation" + ], + "EDAM topic": [ + "Sequence analysis", + "Gene structure" + ], + "Status": "Up-to-date", + "Source": "https://github.com/BrendelGroup/AEGeAn", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "aegean", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean", + "Galaxy wrapper version": "0.16.0", + "Conda id": "aegean", + "Conda version": "0.16.0" + }, + { + "Galaxy wrapper id": "aldex2", + "Galaxy tool ids": [ + "aldex2" + ], + "Description": "Performs analysis Of differential abundance taking sample variation into account", + "bio.tool id": "aldex2", + "bio.tool ids": [ + "aldex2" + ], + "biii": null, + "bio.tool name": "ALDEx2", + "bio.tool description": "A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.", + "EDAM operation": [ + "Statistical inference" + ], + "EDAM topic": [ + "Gene expression", + "Statistics and probability" + ], + "Status": "To update", + "Source": "https://github.com/ggloor/ALDEx_bioc", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "aldex2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", + "Galaxy wrapper version": "1.26.0", + "Conda id": "bioconductor-aldex2", + "Conda version": "1.34.0" + }, + { + "Galaxy wrapper id": "allegro", + "Galaxy tool ids": [ + "allegro" + ], + "Description": "Linkage and haplotype analysis from deCODE", + "bio.tool id": "allegro", + "bio.tool ids": [ + "allegro" + ], + "biii": null, + "bio.tool name": "Allegro", + "bio.tool description": "It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3\u2032 UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). 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Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.", + "EDAM operation": [ + "Sequence assembly validation", + "Sequence trimming", + "Sequence contamination filtering" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ncbi/fcs-gx", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ncbi_fcs_gx", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", + "Galaxy wrapper version": "0.5.0", + "Conda id": "ncbi-fcs-gx", + "Conda version": "0.5.0" + }, + { + "Galaxy wrapper id": "necat", + "Galaxy tool ids": [ + "necat" + ], + "Description": "Error correction and de-novo assembly for ONT Nanopore reads", + "bio.tool id": "necat", + "bio.tool ids": [ + "necat" + ], + "biii": null, + "bio.tool name": "NECAT", + "bio.tool description": "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.", + "EDAM operation": [ + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/xiaochuanle/NECAT", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "necat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat", + "Galaxy wrapper version": "0.0.1_update20200803", + "Conda id": "necat", + "Conda version": "0.0.1_update20200803" + }, + { + "Galaxy wrapper id": "newick_utils", + "Galaxy tool ids": [ + "newick_display" + ], + "Description": "Perform operations on Newick trees", + "bio.tool id": "newick_utilities", + "bio.tool ids": [ + "newick_utilities" + ], + "biii": null, + "bio.tool name": "Newick Utilities", + "bio.tool description": "The Newick Utilities are a set of command-line tools for processing phylogenetic trees. 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It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.", + "EDAM operation": [ + "Read mapping", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Transcriptomics", + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/TRON-Bioinformatics/seq2HLA", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seq2hla", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla", + "Galaxy wrapper version": "2.3", + "Conda id": "seq2hla", + "Conda version": "2.3" + }, + { + "Galaxy wrapper id": "seqcomplexity", + "Galaxy tool ids": [ + "seqcomplexity" + ], + "Description": "Sequence complexity for raw reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/stevenweaver/seqcomplexity", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity", + "Galaxy wrapper version": "0.1.2", + "Conda id": "seqcomplexity", + "Conda version": "0.1.2" + }, + { + "Galaxy wrapper id": "seqkit", + "Galaxy tool ids": [ + "seqkit_fx2tab", + "seqkit_locate", + "seqkit_sort", + "seqkit_stats", + "seqkit_translate" + ], + "Description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", + "bio.tool id": "seqkit", + "bio.tool ids": [ + "seqkit" + ], + "biii": null, + "bio.tool name": "seqkit", + "bio.tool description": "FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. 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The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.", + "EDAM operation": [ + "DNA transcription", + "Sequence trimming", + "DNA translation", + "Sequence conversion" + ], + "EDAM topic": [ + "Database management", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://bioinf.shenwei.me/seqkit/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit", + "Galaxy wrapper version": "2.8.2", + "Conda id": "seqkit", + "Conda version": "2.8.2" + }, + { + "Galaxy wrapper id": "seqprep", + "Galaxy tool ids": [ + "seqprep" + ], + "Description": "Tool for merging paired-end Illumina reads and trimming adapters.", + "bio.tool id": "seqprep", + "bio.tool ids": [ + "seqprep" + ], + "biii": null, + "bio.tool name": "SeqPrep", + "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", + "EDAM operation": [ + "Nucleic acid design" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly", + "Sequencing", + "Probes and primers" + ], + "Status": "Up-to-date", + "Source": "https://github.com/jstjohn/SeqPrep", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "seqprep", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep", + "Galaxy wrapper version": "1.3.2", + "Conda id": "seqprep", + "Conda version": "1.3.2" + }, + { + "Galaxy wrapper id": "seqsero2", + "Galaxy tool ids": [ + "seqsero2" + ], + "Description": "Salmonella serotype prediction from genome sequencing data", + "bio.tool id": "seqsero2", + "bio.tool ids": [ + "seqsero2" + ], + "biii": null, + "bio.tool name": "SeqSero2", + "bio.tool description": "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)", + "EDAM operation": [ + "Genome indexing", + "Antimicrobial resistance prediction", + "Genome alignment" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Sequence assembly", + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/denglab/SeqSero2", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqsero2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", + "Galaxy wrapper version": "1.3.1", + "Conda id": "seqsero2", + "Conda version": "1.3.1" + }, + { + "Galaxy wrapper id": "seqtk", + "Galaxy tool ids": [ + "seqtk_comp", + "seqtk_cutN", + "seqtk_dropse", + "seqtk_fqchk", + "seqtk_hety", + "seqtk_listhet", + "seqtk_mergefa", + "seqtk_mergepe", + "seqtk_mutfa", + "seqtk_randbase", + "seqtk_sample", + "seqtk_seq", + "seqtk_subseq", + "seqtk_telo", + "seqtk_trimfq" + ], + "Description": "Toolkit for processing sequences in FASTA/Q formats", + "bio.tool id": "seqtk", + "bio.tool ids": [ + "seqtk" + ], + "biii": null, + "bio.tool name": "seqtk", + "bio.tool description": "A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.", + "EDAM operation": [ + "Data handling", + "Sequence file editing" + ], + "EDAM topic": [ + "Data management" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lh3/seqtk", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqtk", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk", + "Galaxy wrapper version": "1.4", + "Conda id": "seqtk", + "Conda version": "1.4" + }, + { + "Galaxy wrapper id": "seqwish", + "Galaxy tool ids": [ + "seqwish" + ], + "Description": "Alignment to variation graph inducer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/seqwish", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish", + "Galaxy wrapper version": "0.7.5", + "Conda id": "seqwish", + "Conda version": "0.7.10" + }, + { + "Galaxy wrapper id": "seurat", + "Galaxy tool ids": [ + "seurat" + ], + "Description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/satijalab/seurat", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "seurat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat", + "Galaxy wrapper version": "4.3.0.1", + "Conda id": "r-seurat", + "Conda version": "3.0.2" + }, + { + "Galaxy wrapper id": "shasta", + "Galaxy tool ids": [ + "shasta" + ], + "Description": "Fast de novo assembly of long read sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/chanzuckerberg/shasta", + "ToolShed categories": [ + "Assembly", + "Nanopore" + ], + "ToolShed id": "shasta", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta", + "Galaxy wrapper version": "0.6.0", + "Conda id": "shasta", + "Conda version": "0.12.0" + }, + { + "Galaxy wrapper id": "shorah", + "Galaxy tool ids": [ + "shorah_amplicon" + ], + "Description": "Reconstruct haplotypes using ShoRAH in amplicon mode", + "bio.tool id": "shorah", + "bio.tool ids": [ + "shorah" + ], + "biii": null, + "bio.tool name": "ShoRAH", + "bio.tool description": "Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.", + "EDAM operation": [ + "Haplotype mapping", + "Variant calling" + ], + "EDAM topic": [ + "Metagenomics", + "Sequencing", + "Genetics" + ], + "Status": "To update", + "Source": "https://github.com/cbg-ethz/shorah/blob/master/README.md", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "shorah_amplicon", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah", + "Galaxy wrapper version": "1.1.3", + "Conda id": "shorah", + "Conda version": "1.99.2" + }, + { + "Galaxy wrapper id": "shovill", + "Galaxy tool ids": [ + "shovill" + ], + "Description": "Faster de novo assembly pipeline based around Spades", + "bio.tool id": "shovill", + "bio.tool ids": [ + "shovill" + ], + "biii": null, + "bio.tool name": "shovill", + "bio.tool description": "Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Genomics", + "Microbiology", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/shovill", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "shovill", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", + "Galaxy wrapper version": "1.1.0", + "Conda id": "shovill", + "Conda version": "1.1.0" + }, + { + "Galaxy wrapper id": "sickle", + "Galaxy tool ids": [ + "sickle" + ], + "Description": "A windowed adaptive trimming tool for FASTQ files using quality", + "bio.tool id": "sickle", + "bio.tool ids": [ + "sickle" + ], + 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It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).", + "EDAM operation": [ + "SNP detection" + ], + "EDAM topic": [ + "DNA polymorphism", + "Genetic variation", + "Nucleic acid sites, features and motifs" + ], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/", + "ToolShed categories": [ + "Genome-Wide Association Study", + "Variant Analysis" + ], + "ToolShed id": "snpeff_sars_cov_2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null + }, + { + "Galaxy wrapper id": "snpfreqplot", + "Galaxy tool ids": [ + "snpfreqplot" + ], + "Description": "Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snpfreqplot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot", + "Galaxy wrapper version": "1.0", + "Conda id": "r-base", + "Conda version": null + }, + { + "Galaxy wrapper id": "socru", + "Galaxy tool ids": [ + "socru" + ], + "Description": "Order and orientation of complete bacterial genomes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/quadram-institute-bioscience/socru", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "socru", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru", + "Galaxy wrapper version": "2.1.7", + "Conda id": "socru", + "Conda version": "2.2.4" + }, + { + "Galaxy wrapper id": "sonneityping", + "Galaxy tool ids": [ + "sonneityping" + ], + "Description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", + "bio.tool id": "sonneityping", + "bio.tool ids": [ + "sonneityping" + ], + "biii": null, + "bio.tool name": "sonneityping", + "bio.tool description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", + "EDAM operation": [ + "Antimicrobial resistance prediction", + "Variant calling", + "Genotyping" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Genotype and phenotype", + "Genetic variation", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/katholt/sonneityping", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sonneityping", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/katholt/sonneityping", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping", + "Galaxy wrapper version": "20210201", + "Conda id": "sonneityping", + "Conda version": "20210201" + }, + { + "Galaxy wrapper id": "spades", + "Galaxy tool ids": [ + "spades_biosyntheticspades", + "spades_coronaspades", + "spades_metaplasmidspades", + "metaspades", + "spades_metaviralspades", + "spades_plasmidspades", + "rnaspades", + "spades_rnaviralspades", + "spades" + ], + "Description": "SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.", + "bio.tool id": "spades", + "bio.tool ids": [ + "coronaspades", + "biosyntheticspades", + "metaviralspades", + "metaspades", + "rnaspades", + "rnaviralspades", + "spades", + "plasmidspades", + "metaplasmidspades" + ], + "biii": null, + "bio.tool name": "SPAdes", + "bio.tool description": "St. Petersburg genome assembler \u2013 is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ablab/spades", + "ToolShed categories": [ + "Assembly", + "RNA", + "Metagenomics" + ], + "ToolShed id": "spades", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades", + "Galaxy wrapper version": "3.15.5", + "Conda id": "spades", + "Conda version": "3.15.5" + }, + { + "Galaxy wrapper id": "spaln", + "Galaxy tool ids": [ + "list_spaln_tables", + "spaln" + ], + "Description": "Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool 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+ "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfflatten", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfgeno2haplo", + "Galaxy tool ids": [ + "vcfgeno2haplo" + ], + "Description": "Convert genotype-based phased alleles into haplotype alleles", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfgeno2haplo", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfgenotypes", + "Galaxy tool ids": [ + "vcfgenotypes" + ], + "Description": "Convert numerical representation of genotypes to allelic.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfgenotypes", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfhethom", + "Galaxy tool ids": [ + "vcfhethom" + ], + "Description": "Count the number of heterozygotes and alleles, compute het/hom ratio.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfhethom", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfleftalign", + "Galaxy tool ids": [ + "vcfleftalign" + ], + "Description": "Left-align indels and complex variants in VCF dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfleftalign", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfprimers", + "Galaxy tool ids": [ + "vcfprimers" + ], + "Description": "Extract flanking sequences for each VCF record", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfprimers", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfrandomsample", + "Galaxy tool ids": [ + "vcfrandomsample" + ], + "Description": "Randomly sample sites from VCF dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfrandomsample", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfselectsamples", + "Galaxy tool ids": [ + "vcfselectsamples" + ], + "Description": "Select samples from a VCF file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfselectsamples", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfsort", + "Galaxy tool ids": [ + "vcfsort" + ], + "Description": "Sort VCF dataset by coordinate", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfsort", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + }, + { + "Galaxy wrapper id": "vcfvcfintersect", + "Galaxy tool ids": [ + "vcfvcfintersect" + ], + "Description": "Intersect two VCF datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfvcfintersect", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9" + } +] \ No newline at end of file diff --git a/results/repositories03.list_tools.tsv b/results/repositories03.list_tools.tsv index 4dea1b27..6022d85e 100644 --- a/results/repositories03.list_tools.tsv +++ b/results/repositories03.list_tools.tsv @@ -1,589 +1,604 @@ -Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu -TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) -abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) -abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr 1.0.14 abritamr 1.0.14 (0/1) (0/1) (0/1) -abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly To update http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss 2.3.6 abyss 2.3.7 (0/1) (1/1) (1/1) -adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) -add_input_name_as_column 83150.0 91.0 addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python (1/1) (0/1) (1/1) -aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) -aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) -allegro allegro Linkage and haplotype analysis from deCODE allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ @VER@.0 allegro 3 (0/1) (0/1) (0/1) -amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) -ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 2.7.22 (0/19) (0/19) (19/19) -amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.11.26 (0/1) (0/1) (1/1) -ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.10.3 anndata 0.6.22.post1 (5/5) (3/5) (5/5) -annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.17.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) -arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) -art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (0/3) -artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) -assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) -augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) -b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) -bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.9.2 (0/1) (1/1) (1/1) -bam_to_scidx 128.0 4.0 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx 1.0.1 openjdk (1/1) (0/1) (1/1) -bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) -bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) -barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 (0/1) (0/1) (0/1) -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 (4/4) (0/4) (4/4) -barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) -basil 266.0 35.0 basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc 1.2.0 anise_basil 1.2.0 (1/1) (0/1) (1/1) -bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) -bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.01 bbmap 39.01 (1/6) (1/6) (5/6) -bcftools 524.0 78.0 bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools 1.15.1 bcftools 1.19 (0/5) (0/5) (0/5) -bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) -beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). GA4GH Beacon Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 (0/3) (0/3) (3/3) -beagle 54.0 10.0 beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e (0/1) (0/1) (1/1) -bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/ 2.4.41 bedops 2.4.41 (1/1) (0/1) (1/1) -bedtools 936832.0 6318.0 bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics To update https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 2.30.0 bedtools 2.31.1 (37/37) (37/37) (37/37) -bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) -berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka 0.2.3 berokka 0.2.3 (0/1) (1/1) (0/1) -binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) -bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! To update https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ 0.20.4 python-bioext 0.21.2 (2/2) (0/2) (2/2) -bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python (1/1) (0/1) (1/1) -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) -bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) -biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) -blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast 1.7.0 magicblast 1.7.0 (0/1) (0/1) (1/1) -blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) -bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 2.5.0 bowtie2 2.5.3 (1/1) (1/1) (1/1) -bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken 2.9 bracken 2.9 (0/1) (0/1) (1/1) -breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc 0.35.5 breseq 0.38.2 (0/1) (1/1) (1/1) -busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.6.1 (1/1) (1/1) (1/1) -bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa 0.7.17 bwa 0.7.17 (2/2) (2/2) (2/2) -bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) -bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) -calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) -calculate_numeric_param 1393.0 8.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param 0.1.0 (0/1) (0/1) (1/1) -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) -cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) -cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) -charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt (0/1) (0/1) (0/1) -checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) -chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) -chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 1.0.7 chopin2 (1/1) (0/1) (0/1) -chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) -circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) -circos 21787.0 1018.0 circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos 0.69.8 circos 0.69.9 (11/11) (11/11) (11/11) -cite_seq_count 18.0 1.0 cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.4 (1/1) (0/1) (1/1) -clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 0.1.12 clair3 1.0.5 (0/1) (0/1) (1/1) -clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins " - clustal2 - " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) -cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit 0.9.10 cnvkit 0.9.10 (0/17) (0/17) (17/17) -codeml 60901.0 29.0 codeml Detects positive selection To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) -cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) -colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) -collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) -collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) -column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.0 python (1/1) (1/1) (1/1) -column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) -column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python (1/1) (1/1) (1/1) -compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) -compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) -concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) -coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) -coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics To update https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm 0.6.1 coverm 0.7.0 (0/2) (0/2) (2/2) -crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) -crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) -crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) -cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt 4.6 cutadapt 4.6 (1/1) (1/1) (1/1) -cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv 1.0.8 cutesv 2.1.0 (0/1) (1/1) (1/1) -cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) -dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) -das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics To update https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool 1.1.6 das_tool 1.1.7 (0/2) (0/2) (2/2) -data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga 1.0.0 python (0/1) (0/1) (0/1) -datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash 1.8 datamash 1.1.0 (3/3) (3/3) (3/3) -decontaminator 99.0 15.0 decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator 1.0.0 numpy (0/1) (0/1) (1/1) -deepmicro 501.0 3.0 deepmicro Representation learning and classification framework " - DeepMicro - " Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 (0/1) (0/1) (1/1) -deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) -deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) -deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) -delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) -deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis Transcriptomics To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) -dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) -diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond 2.0.15 diamond 2.1.8 (3/3) (3/3) (3/3) -diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) -dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. To update https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet 0.1.4 dimet 0.2.1 (0/1) (0/1) (0/1) -disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ disco 1.2 (1/1) (0/1) (1/1) -dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) -dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.4.5 (0/2) (0/2) (2/2) -dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) -ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) -edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) -egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) -emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) -ena_upload 208.0 14.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). To update https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload 0.6.3 ena-upload-cli 0.7.0 (0/1) (1/1) (1/1) -enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch enasearch 0.2.2 (0/5) (0/5) (5/5) -ensembl_vep 2653.0 119.0 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep 110.1 ensembl-vep 111.0 (0/1) (0/1) (1/1) -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ 0.3.2 episcanpy 0.4.0 (2/3) (0/3) (3/3) -exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) -exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) -export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) -extract_genomic_dna 11348.0 285.0 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.10.0 (1/1) (0/1) (1/1) -fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) -fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) -fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy (1/1) (1/1) (1/1) -fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc 1.3 fastani 1.34 (0/1) (0/1) (1/1) -fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files " - fastp - " To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1) -fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc 0.74+galaxy0 fastqc 0.12.1 (1/1) (1/1) (1/1) -fastqe 4333.0 1266.0 fastqe FASTQE To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) -fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) -featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation Sequencing To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) -feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) -fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) -fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) -filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality " - filtlong - " Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) -flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) -flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) -fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ fraggenescan 1.31 (0/1) (1/1) (1/1) -freebayes 153548.0 3059.0 freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes 1.3.6 freebayes 1.3.7 (2/2) (2/2) (2/2) -freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec 11.6 gawk (0/1) (0/1) (1/1) -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.8 (2/4) (0/4) (4/4) -fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd 1.0.2 matplotlib (4/4) (0/4) (0/4) -funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " - funannotate - " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) -gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 4.1.7.0 gatk4 4.4.0.0 (1/1) (0/1) (1/1) -gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy 1.0.0 python (1/1) (0/1) (1/1) -gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) -gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) -genebed_maf_to_fasta 2.0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 (1/1) (1/1) (1/1) -genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ 3.0.0 ghm 3.1 (0/1) (0/1) (0/1) -geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) -genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack numpy (1/1) (0/1) (0/1) -genomescope 2118.0 329.0 genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope 2.0 genomescope2 2.0 (1/1) (1/1) (1/1) -genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) -genrich 3515.0 79.0 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich 0.5+galaxy2 genrich 0.6.1 (1/1) (1/1) (1/1) -get_hrun 4.0 1.0 get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.1 (0/1) (0/1) (1/1) -getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle 1.7.7.0 getorganelle 1.7.7.0 (0/2) (2/2) (2/2) -gfa_to_fa 8274.0 332.0 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa 0.1.2 (1/1) (1/1) (1/1) -gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) -gffcompare 3477.0 381.0 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare 0.12.6 gffcompare 0.12.6 (1/1) (1/1) (1/1) -gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base (5/5) (2/5) (5/5) -ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset 1.0 r-ggupset (0/1) (0/1) (0/1) -glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) -goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) -goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) -gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ @TOOL_VERSION@+galaxy11 r-gprofiler2 (5/5) (0/5) (5/5) -graphembed 63.0 2.0 graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ 2.4 graph_embed 2.4 (1/1) (0/1) (1/1) -graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees To update https://bitbucket.org/nsegata/graphlan/overview Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ graphlan 1.1.3 (2/2) (2/2) (2/2) -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) -gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 357 ucsc-gtftogenepred 447 (1/1) (1/1) (1/1) -gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.1 (1/1) (1/1) (1/1) -gvcftools gvcftools_extract_variants To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools 0.1 gvcftools 0.17.0 (0/1) (0/1) (0/1) -gwastools gwastools_manhattan_plot gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 (0/2) (0/2) (2/2) -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) -hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) -hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog 1.3.6 hapog 1.3.7 (0/1) (0/1) (1/1) -happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) -heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 3.1.3 r-gplots 2.17.0 (1/1) (1/1) (1/1) -heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. bionet BioNet This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) -hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) -hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff 3.1.5 hicstuff 3.2.1 (0/1) (0/1) (0/1) -hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) -hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) -hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ 1.3.1 python-hivclustering 1.6.8 (0/1) (0/1) (0/1) -hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families To update http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 3.3.2 hmmer 3.4 (0/12) (12/12) (12/12) -homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) -htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis To update https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count 0.9.1+galaxy1 htseq 2.0.5 (1/1) (1/1) (1/1) -humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (6/13) (13/13) -hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper 2.1.6 hybpiper 2.1.6 (0/1) (1/1) (0/1) -hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ 2.5.47 hyphy 2.5.59 (17/17) (2/17) (17/17) -hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.1 icescreen 1.3.1 (0/1) (0/1) (0/1) -idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) -idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) -idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download 0.44.1 omero-py 5.11.1 (0/1) (0/1) (1/1) -iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain 1.5.3 instrain 1.8.0 (0/2) (0/2) (2/2) -integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis To update https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder 2.0.2 hmmer 3.4 (0/1) (1/1) (1/1) -intermine_galaxy_exchange 44.0 1.0 galaxy_intermine_exchange InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 (1/1) (1/1) (1/1) -interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) -interval2maf 14.0 3.0 Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.10.0 (1/1) (1/1) (1/1) -intervene 1497.0 136.0 intervene_pairwise, intervene_upset Create pairwise and upset plots intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene 0.6.5 intervene 0.6.5 (2/2) (0/2) (2/2) -iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood To update http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ 2.1.2 iqtree 2.2.6 (1/1) (1/1) (1/1) -irissv 29.0 4.0 irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ 1.0.4 samtools 1.19.2 (0/1) (0/1) (1/1) -isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) -isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) -ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) -iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 (3/3) (3/3) (3/3) -jasminesv 30.0 3.0 jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ 1.0.11 jasminesv 1.1.5 (1/1) (0/1) (1/1) -jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) -jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) -jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.0 (0/1) (1/1) (1/1) -join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 (0/1) (0/1) (0/1) -jq 2312.0 21.0 jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq 1.0 jq 1.5 (1/1) (1/1) (1/1) -jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 (1/1) (0/1) (1/1) -kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ 0.48.0 kallisto 0.50.1 (2/2) (2/2) (2/2) -kc-align kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) -khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) -king 5.0 3.0 king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ 2.2.7 king 2.2.7 (0/1) (0/1) (1/1) -kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) -kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma 1.2.21 kma 1.4.9 (0/1) (0/1) (1/1) -kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) -kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) -kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (0/1) (1/1) -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 (1/6) (2/6) (6/6) -krocus krocus Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (0/1) -last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last 1205 last 1526 (0/5) (0/5) (5/5) -lastz 83331.0 188.0 lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz 1.04.22 lastz 1.04.22 (2/2) (2/2) (2/2) -lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie 1.0.2 lcr_genie (0/1) (0/1) (0/1) -legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) -length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) -limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics To update http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom 3.50.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) -lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot 1.4.0 r-base (0/1) (0/1) (1/1) -links 405.0 77.0 links Scaffold genome assemblies with long reads. links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) -lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq 2.1.5 lofreq 2.1.5 (5/5) (5/5) (5/5) -lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) -lumpy_sv 358.0 50.0 lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv 0.3.1 lumpy-sv 0.3.1 (0/2) (0/2) (2/2) -m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) -maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. Up-to-date http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 0.99.12 maaslin2 0.99.12 (0/1) (0/1) (1/1) -macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) -maf_stats 8.0 2.0 maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 (1/1) (1/1) (1/1) -mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck 0.5.9.2 mageck 0.5.9.5 (3/5) (5/5) (5/5) -maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) -malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt 0.5.3 malt 0.61 (0/1) (0/1) (1/1) -map_param_value 1528.0 9.0 map_param_value Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value 0.2.0 (1/1) (0/1) (1/1) -mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) -mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) -masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) -maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ maxbin2 2.2.7 (1/1) (1/1) (1/1) -mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) -medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) -megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) -megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.24.20 (0/7) (0/7) (7/7) -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_fimo meme_fimo A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. Sequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculation Sequence analysis, Genetic variation, Statistics and probability, Data mining To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) -meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) -meningotype meningotype Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) -merlin merlin Pedigree Analysis package merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) -merqury 2483.0 244.0 merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury 1.3 merqury 1.3 (1/1) (1/1) (1/1) -meryl 6785.0 350.0 meryl Meryl a k-mer counter. meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) -metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ 2.15 metabat2 2.15 (1/2) (1/2) (2/2) -metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) -metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) -metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics Up-to-date https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ 4.0.6 metaphlan 4.0.6 (1/4) (2/4) (4/4) -migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) -minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) -miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) -minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 2.26 minimap2 2.26 (1/1) (1/1) (1/1) -miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot 0.12 miniprot 0.12 (0/2) (0/2) (2/2) -mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 (0/1) (0/1) (1/1) -mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) -mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos 1.1.5 mitos 2.1.7 (1/2) (1/2) (2/2) -mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Taxonomic classification Immunoproteins, genes and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) -moabs 317.0 19.0 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.0 (0/1) (0/1) (1/1) -mosdepth 262.0 21.0 mosdepth fast and flexible BAM/CRAM depth calculation To update https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth 0.3.5 mosdepth 0.3.6 (0/1) (0/1) (1/1) -mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) -msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) -multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) -multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules To update https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea 1.8.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) -multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation Sequencing, Bioinformatics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc 1.11 multiqc 1.19 (1/1) (1/1) (1/1) -mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mumer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) -mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) -mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) -naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) -nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) -nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments To update https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ 1.41.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) -nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) -ncbi_acc_download 5487.0 688.0 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 (1/1) (1/1) (1/1) -ncbi_datasets 3177.0 667.0 datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets 15.19.1 ncbi-datasets-cli (2/2) (0/2) (2/2) -ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct 16.2 entrez-direct 16.2 (0/3) (0/3) (0/3) -ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils 1.70 python (0/8) (0/8) (8/8) -ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (0/1) -necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) -newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) -nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) -ngmlr 1266.0 21.0 ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr 0.2.7 ngmlr 0.2.7 (0/1) (0/1) (1/1) -ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils ngsutils 0.5.9 (1/1) (1/1) (1/1) -nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) -novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty 4.3.1 novoplasty 4.3.3 (0/1) (1/1) (1/1) -nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) -obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) -ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1) -odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.4 (0/2) (0/2) (2/2) -ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.2 (0/4) (0/4) (4/4) -onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18) -optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1) -optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) -orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) -orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) -packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) -pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) -parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) -pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) -pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 (0/1) (0/1) (0/1) -pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping To update https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 1.10.0 pbmm2 1.13.1 (0/1) (0/1) (0/1) -pe_histogram 4180.0 312.0 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram 1.0.1 openjdk (1/1) (1/1) (1/1) -pear 4305.0 150.0 iuc_pear PEAR evaluates all possible paired-end read overlaps pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear 0.9.6 pear 0.9.6 (1/1) (1/1) (1/1) -pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) (0/1) +abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) +abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.7 abyss 2.3.7 (0/1) (1/1) (1/1) (0/1) +adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) (0/1) +add_input_name_as_column 83150.0 91.0 addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python (1/1) (0/1) (1/1) (0/1) +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) (4/4) +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) (0/1) +allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 (0/1) (0/1) (0/1) (0/1) +amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) (0/1) +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.6 (0/19) (0/19) (19/19) (0/19) +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.12.8 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) (1/1) +ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) (0/1) +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.3 anndata 0.6.22.post1 (5/5) (4/5) (5/5) (0/5) +annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) (1/1) +arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) (0/3) +art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (3/3) (0/3) +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) (0/2) +assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) (1/1) +augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) (2/2) +b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) (0/1) +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.3 bakta 1.9.3 (0/1) (1/1) (1/1) (1/1) +bam_to_scidx 128.0 4.0 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) +bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) (1/1) +bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (2/4) (4/4) (0/4) +bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) (0/2) +bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) (2/2) +barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 (0/1) (0/1) (0/1) (0/1) +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 (4/4) (0/4) (4/4) (0/4) +barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) (1/1) +basil 266.0 35.0 basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 (1/1) (0/1) (1/1) (0/1) +bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) (0/1) +bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) (0/1) +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. bbmap bbmap, bbtools BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) (0/6) +bcftools 524.0 78.0 bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.20 (0/5) (0/5) (0/5) (0/5) +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) (0/7) +beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 (0/3) (0/3) (3/3) (0/3) +beagle 54.0 10.0 beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e (0/1) (0/1) (1/1) (0/1) +bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 (1/1) (0/1) (1/1) (0/1) +bedtools 936832.0 6318.0 bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics Up-to-date https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.31.1 bedtools 2.31.1 (37/37) (37/37) (37/37) (37/37) +bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) (0/1) +berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. To update https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka (0/1) (1/1) (0/1) (0/1) +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF BiG-SCAPE BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 (0/1) (0/1) (1/1) (0/1) +binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) (0/1) +bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! To update https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.2 python-bioext (2/2) (0/2) (2/2) (0/2) +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python (1/1) (0/1) (1/1) (0/1) +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (6/6) (0/6) +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) (1/1) +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) +biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) (0/1) +blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 (0/1) (0/1) (1/1) (0/1) +blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (0/1) +bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping To update http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.4 (1/1) (1/1) (1/1) (1/1) +bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (1/1) (1/1) (1/1) (1/1) +breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.38.3 (0/1) (1/1) (1/1) (0/1) +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) +bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.18 bwa 0.7.18 (2/2) (2/2) (2/2) (2/2) +bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) (1/1) +bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads Up-to-date https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.7 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) +cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) +calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) (0/1) +calculate_numeric_param 1393.0 8.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 (0/1) (0/1) (1/1) (0/1) +cami_amber cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments Up-to-date https://github.com/CAMI-challenge/AMBER Metagenomics cami_amber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 2.0.4 cami-amber 2.0.4 (0/3) (0/3) (0/3) (0/3) +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) +cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) +cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) (0/1) +charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt (0/1) (0/1) (0/1) (0/1) +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) (10/10) +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) (0/2) +chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.5 (0/8) (0/8) (8/8) (0/8) +chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) (0/5) +chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.8.post1 chopin2 (1/1) (0/1) (0/1) (0/1) +chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) (1/1) +circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) +circos 21787.0 1018.0 circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 (11/11) (11/11) (11/11) (11/11) +cite_seq_count 18.0 1.0 cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.4 (1/1) (0/1) (1/1) (0/1) +clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 0.1.12 clair3 1.0.8 (0/1) (0/1) (1/1) (0/1) +clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) +cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket (0/1) (0/1) (1/1) (0/1) +cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.0.4 cnv-vcf2json (0/1) (0/1) (1/1) (0/1) +cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.11 cnvkit 0.9.11 (0/17) (0/17) (17/17) (0/17) +codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation To update https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.2 (2/3) (0/3) (3/3) (0/3) +colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) +collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) (1/1) +collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) (1/1) +column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.0 python (1/1) (1/1) (1/1) (1/1) +column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) (1/1) +column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python (1/1) (1/1) (1/1) (1/1) +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) +compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) (1/1) +compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) (0/1) +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis cosg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 (0/1) (0/1) (0/1) (0/1) +coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) (0/1) +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) +crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) (0/1) +crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) (0/1) +crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) (0/7) +cuffcompare 1130.0 65.0 cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffdiff 5831.0 228.0 cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 (1/1) (0/1) (1/1) (0/1) +cufflinks 32218.0 319.0 cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffmerge 3292.0 122.0 cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffnorm 660.0 27.0 cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +cuffquant 688.0 18.0 cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.8 cutadapt 4.8 (1/1) (1/1) (1/1) (1/1) +cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 1.0.8 cutesv (0/1) (1/1) (1/1) (0/1) +cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) (0/1) +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) +das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 (0/2) (0/2) (2/2) (2/2) +data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python (0/1) (0/1) (0/1) (0/1) +datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 (3/3) (3/3) (3/3) (3/3) +decontaminator 99.0 15.0 decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +deepmicro 501.0 3.0 deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 (0/1) (0/1) (1/1) (0/1) +deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) (1/1) +deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) (0/1) +deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) (1/1) +delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) (0/6) +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) +dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) +diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) (1/1) +dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 (0/1) (0/1) (0/1) (0/1) +disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 (1/1) (0/1) (1/1) (0/1) +dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) (0/1) +dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) (0/1) +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.3.5 dram 1.5.0 (0/5) (0/5) (5/5) (0/5) +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.5.0 drep 3.5.0 (0/2) (0/2) (2/2) (2/2) +dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) (1/1) +ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) (0/2) +edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 (1/1) (1/1) (1/1) (1/1) +egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) (0/1) +emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) (107/107) +ena_upload 208.0 14.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). Up-to-date https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.1 ena-upload-cli 0.7.1 (0/1) (1/1) (1/1) (1/1) +enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 (0/5) (0/5) (5/5) (0/5) +ensembl_vep 2653.0 119.0 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 110.1 ensembl-vep 112.0 (0/1) (0/1) (1/1) (0/1) +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 (2/3) (0/3) (3/3) (0/3) +exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) (0/1) +exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) (1/1) +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) (1/1) +extract_genomic_dna 11348.0 285.0 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) (0/1) +fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 377 ucsc-fasplit 377 (1/1) (1/1) (1/1) (1/1) +fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 (0/1) (1/1) (0/1) (0/1) +fasta_formatter 2912.0 68.0 cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fasta_nucleotide_changer 774.0 29.0 cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy (1/1) (1/1) (1/1) (1/1) +fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Genome alignment, Sequence similarity search Microbiology, Genetic variation To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 (0/1) (0/1) (1/1) (1/1) +fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) To update https://github.com/thegenemyers/FASTK Assembly fastk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 1.0.0 fastk 1.0 (0/1) (0/1) (1/1) (0/1) +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 (1/1) (1/1) (1/1) (1/1) +fastq_combiner 8676.0 66.0 fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_filter 14222.0 266.0 fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_groomer 94802.0 1028.0 fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_manipulation 2503.0 69.0 fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_masker_by_quality 170.0 16.0 fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_deinterlacer 8410.0 122.0 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_interlacer 17024.0 1087.0 fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_joiner 16635.0 245.0 fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_splitter 3092.0 196.0 fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_quality_boxplot 1175.0 51.0 cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_converter 220.0 11.0 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_filter 15153.0 1509.0 cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_stats 4246.0 221.0 fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_to_fasta 13599.0 419.0 cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_to_tabular 12593.0 93.0 fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_trimmer 9757.0 210.0 fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy0 fastqc 0.12.1 (1/1) (1/1) (1/1) (1/1) +fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) +fastqtofasta 178172.0 1371.0 fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (0/1) +fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) +fastx_artifacts_filter 1809.0 27.0 cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_barcode_splitter 16589.0 128.0 cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_clipper 3321.0 96.0 cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_collapser 61218.0 114.0 cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_nucleotides_distribution 249.0 25.0 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_quality_statistics 2162.0 63.0 cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_renamer 2280.0 68.0 cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_reverse_complement 10831.0 156.0 cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_trimmer 13148.0 205.0 cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 (1/1) (1/1) (1/1) (0/1) +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) +feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (1/1) (1/1) (1/1) +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) (0/2) +fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) (1/1) +filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) (1/1) +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) (0/2) +flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) (0/1) +fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 (0/1) (1/1) (1/1) (1/1) +freebayes 153548.0 3059.0 freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.6 freebayes 1.3.7 (2/2) (2/2) (2/2) (2/2) +freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk (0/1) (0/1) (1/1) (0/1) +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.4.4 freyja 1.5.0 (2/4) (0/4) (4/4) (0/4) +fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib (4/4) (0/4) (0/4) (0/4) +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) (5/5) +gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 (1/1) (0/1) (1/1) (0/1) +gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python (1/1) (0/1) (1/1) (0/1) +gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) (0/1) +gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) (2/3) +genebed_maf_to_fasta 2.0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 (1/1) (1/1) (1/1) (1/1) +genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 (0/1) (0/1) (0/1) (0/1) +geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) (0/1) +genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy (1/1) (0/1) (0/1) (0/1) +genomescope 2118.0 329.0 genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0 genomescope2 2.0 (1/1) (1/1) (1/1) (1/1) +genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) (0/1) +genrich 3515.0 79.0 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 (1/1) (1/1) (1/1) (0/1) +get_hrun 4.0 1.0 get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.1 (0/1) (0/1) (1/1) (0/1) +getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 (0/2) (2/2) (2/2) (0/2) +gfa_to_fa 8274.0 332.0 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 (1/1) (1/1) (1/1) (1/1) +gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (1/1) +gffcompare 3477.0 381.0 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 (1/1) (1/1) (1/1) (1/1) +gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) (1/1) +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) (5/5) +ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset (0/1) (0/1) (0/1) (0/1) +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) (0/8) +goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) (2/2) +goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) (1/1) +gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 (5/5) (0/5) (5/5) (0/5) +graphembed 63.0 2.0 graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 (1/1) (0/1) (1/1) (0/1) +graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 (2/2) (2/2) (2/2) (2/2) +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.3.2 gtdbtk 2.4.0 (0/1) (1/1) (1/1) (0/1) +gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 447 (1/1) (1/1) (1/1) (1/1) +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 (1/1) (1/1) (1/1) (0/1) +gvcftools gvcftools_extract_variants To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 (0/1) (0/1) (0/1) (0/1) +gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) (0/1) +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) +hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.4 hapcut2 1.3.4 (0/1) (1/1) (0/1) (0/1) +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) +happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) (0/1) +heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.1.3.1 r-gplots 2.17.0 (1/1) (1/1) (1/1) (1/1) +heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz bionet, heinz Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.2 hicexplorer 3.7.4 (0/40) (5/40) (40/40) (4/40) +hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.1.5 hicstuff 3.2.2 (0/1) (0/1) (0/1) (0/1) +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) +hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) (1/1) +hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.6.8 (0/1) (0/1) (0/1) (0/1) +hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 (0/12) (12/12) (12/12) (12/12) +homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) (4/5) +htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 (1/1) (1/1) (1/1) (1/1) +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.8 humann 3.8 (6/13) (12/13) (13/13) (13/13) +hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics To update https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.1.7 (0/1) (1/1) (1/1) (0/1) +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.62 (17/17) (2/17) (17/17) (2/17) +hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) (0/1) +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 (0/1) (0/1) (0/1) (0/1) +idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) (3/3) +idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) (0/1) +idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.44.1 omero-py 5.11.1 (0/1) (0/1) (1/1) (1/1) +iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) (0/1) +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.9.0 (0/2) (0/2) (2/2) (0/2) +integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.3 integron_finder 2.0.3 (0/1) (1/1) (1/1) (1/1) +intermine_galaxy_exchange 44.0 1.0 galaxy_intermine_exchange InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) (1/1) +interval2maf 14.0 3.0 Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +intervene 1497.0 136.0 intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 (2/2) (0/2) (2/2) (0/2) +iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics Up-to-date http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.3.4 iqtree 2.3.4 (1/1) (1/1) (1/1) (0/1) +irissv 29.0 4.0 irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.5 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) (1/1) +isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) (1/1) +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) (5/5) +iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 (3/3) (3/3) (3/3) (0/3) +jasminesv 30.0 3.0 jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 (1/1) (0/1) (1/1) (0/1) +jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) (2/2) +jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.4.15 (1/1) (1/1) (1/1) (1/1) +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) (1/1) +join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 (0/1) (0/1) (0/1) (0/1) +jq 2312.0 21.0 jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 (1/1) (1/1) (1/1) (1/1) +jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 (1/1) (0/1) (1/1) (0/1) +kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.50.1 (2/2) (2/2) (2/2) (2/2) +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) (0/1) +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) (0/8) +king 5.0 3.0 king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 (0/1) (0/1) (1/1) (0/1) +kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) (0/1) +kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.2.21 kma 1.4.14 (0/1) (0/1) (1/1) (0/1) +kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) (1/1) +kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) +kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) (1/1) +kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (1/1) (1/1) (0/1) +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 (1/6) (6/6) (6/6) (6/6) +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (1/1) (0/1) +last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1542 (0/5) (0/5) (5/5) (5/5) +lastz 83331.0 188.0 lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 (2/2) (2/2) (2/2) (2/2) +lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie (0/1) (0/1) (0/1) (0/1) +legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) (0/1) +length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) (1/1) +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) (1/1) +lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base (0/1) (0/1) (1/1) (0/1) +links 405.0 77.0 links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) (0/1) +lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 (5/5) (5/5) (5/5) (4/5) +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) (0/1) +lumpy_sv 358.0 50.0 lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 (0/2) (0/2) (2/2) (0/2) +m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) (0/1) +maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 0.99.12 maaslin2 1.16.0 (0/1) (0/1) (1/1) (0/1) +macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) (9/9) +maf_stats 8.0 2.0 maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 (1/1) (1/1) (1/1) (1/1) +mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 (3/5) (5/5) (5/5) (5/5) +maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) +malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 (0/1) (0/1) (1/1) (0/1) +map_param_value 1528.0 9.0 map_param_value Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 (1/1) (0/1) (1/1) (0/1) +mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) +mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) +mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) +masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) (0/1) +maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) +mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) (3/4) +megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) +megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (1/1) +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_meme, meme_fimo meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) (0/4) +meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) (0/1) +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) +merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) (0/1) +merqury 2483.0 244.0 merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 (2/2) (2/2) (2/2) (2/2) +meryl 6785.0 350.0 meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 (0/7) (0/7) (0/7) (0/7) +metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.15 (2/2) (1/2) (2/2) (2/2) +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) +metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.1 (1/4) (2/4) (4/4) (4/4) +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) +migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) +minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) +miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) +minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 (1/1) (1/1) (1/1) (1/1) +miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) +mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) +mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) +mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) (0/1) +mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 (1/2) (1/2) (2/2) (0/2) +mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) (2/2) +moabs 317.0 19.0 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 (0/1) (0/1) (1/1) (0/1) +mosdepth 262.0 21.0 mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.8 mosdepth 0.3.8 (0/1) (0/1) (1/1) (0/1) +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) (129/129) +msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) (0/1) +multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) (0/1) +multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.22.2 (1/1) (1/1) (1/1) (1/1) +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) (6/6) +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) +mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) (0/1) +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) (0/3) +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) +nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) +ncbi_acc_download 5487.0 688.0 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 (1/1) (1/1) (1/1) (1/1) +ncbi_datasets 3177.0 667.0 datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.6.0 ncbi-datasets-cli (2/2) (0/2) (2/2) (2/2) +ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 21.6 entrez-direct 21.6 (0/3) (0/3) (0/3) (0/3) +ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python (0/8) (0/8) (8/8) (0/8) +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). ncbi_fcs ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) +necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) (0/1) +newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) +nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) +ngmlr 1266.0 21.0 ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 (0/1) (0/1) (1/1) (0/1) +ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 (1/1) (1/1) (1/1) (1/1) +nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) (1/1) +novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 (0/1) (1/1) (1/1) (1/1) +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) +ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1) (0/1) +odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.8.6 (0/2) (0/2) (2/2) (2/2) +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4) (0/4) +onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18) (0/18) +optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1) (0/1) +optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) (0/1) +orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) +packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) (0/1) +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 (5/5) (0/5) (5/5) (0/5) +pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) +parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) +pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) +pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 (0/1) (0/1) (0/1) (0/1) +pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.13.1 pbmm2 1.13.1 (0/1) (0/1) (1/1) (0/1) +pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 (1/1) (0/1) (1/1) (0/1) +pe_histogram 4180.0 312.0 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.1 openjdk (1/1) (1/1) (1/1) (1/1) +peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python (0/1) (0/1) (1/1) (0/1) +pear 4305.0 150.0 iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 (1/1) (1/1) (1/1) (0/1) +pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " pharokka - " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " - pharokka - " (0/1) (1/1) (1/1) -phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3) -phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) -picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_fastqtosam picard_fastqtosam Create an unaligned BAM file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard 2.18.2 picard 3.1.1 (31/31) (31/31) (31/31) -pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (0/1) (1/1) -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) -picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) -pilon 7942.0 467.0 pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon 1.20.1 pilon 1.24 (1/1) (1/1) (1/1) -pipelign 983.0 83.0 pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign 0.2 pipelign 0.2 (1/1) (0/1) (1/1) -pizzly 208.0 16.0 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ 0.37.3.1 pizzly 0.37.3 (1/1) (0/1) (1/1) -plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) -plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) -plink 669.0 46.0 plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink 1.90b6.21 plink 1.90b6.21 (0/1) (0/1) (1/1) -polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) -porechop 185468.0 1046.0 porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop porechop 0.2.4 (1/1) (1/1) (1/1) -poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools 0.6.1a1 poretools 0.6.1a1 (13/13) (13/13) (13/13) -presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) -pretext pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext 0.1.9 pretextmap 0.1.9 (2/2) (2/2) (2/2) -prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) -progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) -prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) -prot-scriber prot_scriber Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber 0.1.4 prot-scriber 0.1.5 (0/1) (0/1) (1/1) -proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Homology-based gene prediction Phylogeny Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) -psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass 1.0.3 psiclass 1.0.3 (0/1) (0/1) (1/1) -pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) -purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) -pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 5.0.2 pyega3 5.1.0 (1/1) (0/1) (1/1) -pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks 3.8 pygenometracks 3.8 (1/1) (1/1) (1/1) -pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) -qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) -qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/2) (0/2) (2/2) -qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 (0/32) (0/32) (32/32) -qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) -qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (3/4) (4/4) -quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) -query_impc 1.0 query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests (0/1) (0/1) (1/1) -query_tabular 20860.0 168.0 filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.0 python (3/3) (3/3) (3/3) -quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 0.2.3 r-raceid 0.1.3 (5/5) (4/5) (5/5) -ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) -rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) -raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) -raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) -rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.6 (0/1) (0/1) (1/1) -read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) -recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.13.2 recentrifuge 1.13.2 (0/1) (0/1) (1/1) -red 578.0 88.0 red Red (REpeat Detector) Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) -repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) -repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) -repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 matplotlib (1/1) (0/1) (0/1) -reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 1.4.2 r-reshape2 (2/2) (0/2) (2/2) -resize_coordinate_window 85.0 5.0 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window 1.0.2 python (1/1) (0/1) (1/1) -rgcca 44.0 3.0 rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca 3.0.2 rgccacmd 3.0.3 (1/1) (0/1) (1/1) -rgrnastar 416677.0 3843.0 rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar 2.7.10b star 2.7.11a (2/2) (2/2) (2/2) -ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) -rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast 2.2.3 rnaquast 2.2.3 (0/1) (0/1) (1/1) -roary 12225.0 656.0 roary Roary the pangenome pipeline roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) -rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor 3.2.1 rp2biosensor (0/1) (0/1) (0/1) -rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths 1.5.1 rp2paths (0/1) (0/1) (0/1) -rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign 1.1.1 rpbasicdesign (0/1) (0/1) (0/1) -rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba 5.12.3 rptools (0/1) (0/1) (0/1) -rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools 5.13.1 rptools (0/5) (0/5) (0/5) -rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser 2.5.2 rrparser (0/1) (0/1) (0/1) -rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc 5.0.1 rseqc 5.0.3 (22/22) (22/22) (22/22) -ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) -salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) -samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) -sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa 0.0.8 sansa 0.0.8 (0/1) (0/1) (1/1) -sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) -sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) -sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc 0.1.13 sbml2sbol (0/1) (0/1) (0/1) -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (4/5) (5/5) -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ 0.0.7 r-sceasy 0.0.7 (1/1) (0/1) (1/1) -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) -scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) -scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) -scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) -seacr 3693.0 50.0 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr 1.3 seacr 1.3 (1/1) (0/1) (1/1) -selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 (0/1) (0/1) (0/1) -semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin 2.0.2 semibin 2.0.2 (0/6) (0/6) (6/6) -seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) -seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) -seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.6.1 (0/3) (0/3) (3/3) -seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 1.2.1 seqsero2 1.2.1 (0/1) (0/1) (1/1) -seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) -seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ 0.7.5 seqwish 0.7.9 (0/1) (0/1) (1/1) -seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) -shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) -shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) -shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) -sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) -simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext 0.0.2 r-argparse 1.0.1 (0/4) (2/4) (4/4) -sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto 0.9.0 sinto 0.10.0 (2/2) (0/2) (2/2) -slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) -sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) -smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 (0/1) (0/1) (1/1) -smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) -snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) -sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc 1.0.12 sniffles 2.2 (1/1) (1/1) (1/1) -snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) -snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) -snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists 0.8.2 snp-dists 0.8.2 (1/1) (1/1) (1/1) -snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites 2.5.1 snp-sites 2.5.1 (1/1) (1/1) (1/1) -snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff (1/1) (1/1) (1/1) -snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ 1.0 r-base (1/1) (1/1) (1/1) -socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) -sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) -spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) -spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln 2.4.9 python (2/2) (0/2) (2/2) -spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine 2.1 spotyping 2.1 (0/1) (0/1) (1/1) -spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools 3.0.8 sra-tools 3.0.10 (3/3) (3/3) (3/3) -srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 0.2.0 samtools 1.19.2 (0/1) (0/1) (1/1) -stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) -stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) -star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.12.0 (1/1) (1/1) (1/1) -straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model Up-to-date https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.2 (0/3) (0/3) (0/3) -strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka 2.9.10 strelka 2.9.10 (2/2) (0/2) (2/2) -stringtie 167659.0 2165.0 stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie 2.2.1 stringtie 2.2.1 (2/2) (2/2) (2/2) -structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) -structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) -swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ 1.0 swiftlink 1.0 (0/1) (0/1) (0/1) -syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) -table_compute 208652.0 741.0 table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas (1/1) (1/1) (1/1) -tag_pileup_frequency 164.0 7.0 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency 1.0.2 openjdk (1/1) (0/1) (1/1) -tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) -taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) -taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) -tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler 4.4.1 tb-profiler 5.0.1 (1/1) (1/1) (1/1) -tb_variant_filter 19252.0 209.0 tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 (1/1) (1/1) (1/1) -tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) -tbvcfreport 2290.0 167.0 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport 0.1.10 tbvcfreport 0.1.10 (1/1) (1/1) (1/1) -te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ 1.0.1 samtools 1.19.2 (0/1) (0/1) (1/1) -telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) -tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) -tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) -tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) -tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) -transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 (5/5) (2/5) (5/5) -transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) -trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) -trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (11/13) (13/13) -trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler 0.5.4 trycycler 0.5.4 (0/5) (5/5) (5/5) -tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra 1.1.2 tsebra 1.1.2.2 (0/1) (0/1) (1/1) -tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) -tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) -ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l 377 ucsc-blat 445 (0/1) (0/1) (0/1) -fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit 377 ucsc-fasplit 377 (1/1) (1/1) (1/1) -fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf 448 ucsc-fatovcf 448 (1/1) (0/1) (1/1) -twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa 377 ucsc-twobittofa 455 (1/1) (0/1) (1/1) -wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig 447 ucsc-wigtobigwig 447 (0/1) (0/1) (1/1) -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 (5/5) (3/5) (5/5) -unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) -usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) -valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet valet 1.0 (1/1) (0/1) (1/1) -vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) -vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) -variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) -varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (1/3) (3/3) -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP 1.1.1 varvamp 1.1.1 (0/1) (0/1) (0/1) -vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF Up-to-date Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf 1.6.21 vcf2maf 1.6.21 (0/1) (1/1) (1/1) -vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation To update https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ 0.3.3 vcfanno 0.3.5 (0/1) (0/1) (1/1) -vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto 0.17.17 velocyto.py 0.17.17 (1/1) (0/1) (1/1) -velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) -velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) -verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko 1.3.1 verkko 1.4.1 (0/1) (0/1) (1/1) -vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg 1.23.0 vg 1.54.0 (0/3) (0/3) (3/3) -virhunter 234.0 40.0 virhunter Deep Learning method for novel virus detection in sequencing data virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter 1.0.0 numpy (0/1) (0/1) (1/1) -volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) -vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch 2.8.3 vsearch 2.27.0 (8/8) (8/8) (8/8) -vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp 3.0.6 pysam 0.22.0 (0/5) (0/5) (0/5) -weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) -weblogo3 2370.0 74.0 rgweblogo3 Sequence Logo generator for fasta weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 3.5.0 weblogo 3.7.9 (1/1) (1/1) (1/1) -windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ 1.0 blast 2.15.0 (0/2) (2/2) (2/2) -winnowmap 248.0 27.0 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap 2.03 winnowmap 2.03 (0/1) (0/1) (1/1) -xpath 234.0 3.0 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) -yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) -zerone 90.0 2.0 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) -bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) -bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) -bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (0/4) (4/4) -biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) -cuffcompare 1130.0 65.0 cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffdiff 5831.0 228.0 cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 (1/1) (0/1) (1/1) -cufflinks 32218.0 319.0 cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffmerge 3292.0 122.0 cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffnorm 660.0 27.0 cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -cuffquant 688.0 18.0 cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) -fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 (0/1) (1/1) (0/1) -fasta_formatter 2912.0 68.0 cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fasta_nucleotide_changer 774.0 29.0 cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_boxplot 1175.0 51.0 cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_converter 220.0 11.0 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_quality_filter 15153.0 1509.0 cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_to_fasta 13599.0 419.0 cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_artifacts_filter 1809.0 27.0 cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_barcode_splitter 16589.0 128.0 cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_clipper 3321.0 96.0 cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_collapser 61218.0 114.0 cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_nucleotides_distribution 249.0 25.0 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_quality_statistics 2162.0 63.0 cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_renamer 2280.0 68.0 cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_reverse_complement 10831.0 156.0 cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastx_trimmer 13148.0 205.0 cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) -fastq_combiner 8676.0 66.0 fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_filter 14222.0 266.0 fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_groomer 94802.0 1028.0 fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_manipulation 2503.0 69.0 fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_masker_by_quality 170.0 16.0 fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_deinterlacer 8410.0 122.0 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_interlacer 17024.0 1087.0 fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_joiner 16635.0 245.0 fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_paired_end_splitter 3092.0 196.0 fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_stats 4246.0 221.0 fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_to_tabular 12593.0 93.0 fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastq_trimmer 9757.0 210.0 fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -fastqtofasta 178172.0 1371.0 fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -tabular_to_fastq 7388.0 200.0 tabular_to_fastq Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) -kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ kraken 1.1.1 (5/5) (5/5) (5/5) -kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) -samtools To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools 1.15.1 samtools 1.19.2 (0/1) (0/1) (0/1) -snpeff 101254.0 2843.0 snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff biopython 1.70 (5/5) (5/5) (5/5) -snpsift 5109063.0 1185.0 snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift snpsift 5.2 (8/8) (8/8) (8/8) -snpsift_dbnsfp 46.0 11.0 snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 (1/1) (0/1) (1/1) -snpsift_genesets 390.0 11.0 snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ snpsift 5.2 (1/1) (0/1) (1/1) -vcf2tsv 167913.0 352.0 vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfaddinfo 357.0 8.0 vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfallelicprimitives 15803.0 286.0 vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfannotate 2181.0 77.0 vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfannotategenotypes 192.0 28.0 vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfbedintersect 3217.0 80.0 vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfbreakcreatemulti 471.0 13.0 vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcheck 675.0 39.0 vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcombine 1695.0 99.0 vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfcommonsamples 244.0 14.0 vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfdistance 564.0 40.0 vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance vcflib 1.0.9 (1/1) (1/1) (1/1) -vcffilter 44444.0 882.0 vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter vcflib 1.0.9 (1/1) (1/1) (1/1) -vcffixup 917.0 71.0 vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfflatten 177.0 6.0 vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfgeno2haplo 718.0 36.0 vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfgenotypes 451.0 48.0 vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfhethom 1370.0 90.0 vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfleftalign 279.0 10.0 vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfprimers 708.0 12.0 vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfrandomsample 159.0 5.0 vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfselectsamples 854.0 29.0 vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfsort 1852.0 63.0 vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort vcflib 1.0.9 (1/1) (1/1) (1/1) -vcfvcfintersect 972774.0 265.0 vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.9 (1/1) (1/1) (1/1) + " (0/1) (1/1) (1/1) (0/1) +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) +phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) +picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_fastqtosam, picard_replacesamheader, picard_samtofastq, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31) (31/31) +pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (1/1) (1/1) (0/1) +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) +pilon 7942.0 467.0 pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 (1/1) (1/1) (1/1) (1/1) +pipelign 983.0 83.0 pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 (1/1) (0/1) (1/1) (0/1) +pizzly 208.0 16.0 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 (1/1) (0/1) (1/1) (0/1) +plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) +plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) +plink 669.0 46.0 plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 (1/1) (0/1) (1/1) (1/1) +polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) +porechop 185468.0 1046.0 porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 (1/1) (1/1) (1/1) (0/1) +poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 (13/13) (13/13) (13/13) (0/13) +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) (0/11) +pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 (3/3) (2/3) (3/3) (0/3) +prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) (1/1) +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) +progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) (0/2) +prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) +prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.5 prot-scriber 0.1.5 (0/1) (0/1) (1/1) (0/1) +proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) (0/3) +psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 (0/1) (0/1) (1/1) (0/1) +pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) (0/1) +purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) (0/1) +pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) +pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 (1/1) (0/1) (1/1) (0/1) +pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows To update https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.9 (1/1) (1/1) (1/1) (1/1) +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) (0/1) +qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) (0/1) +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_add_on, qiime_core qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 (0/2) (0/2) (2/2) (2/2) +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 (0/32) (0/32) (32/32) (32/32) +qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts To update http://www.qiime.org Metagenomics qiime_extract_viz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0.1.0 unzip (0/1) (0/1) (1/1) (0/1) +qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) (0/1) +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (4/4) (4/4) (1/4) +quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) (1/1) +query_impc 1.0 query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests (0/1) (0/1) (1/1) (0/1) +query_tabular 20860.0 168.0 filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.0 python (3/3) (3/3) (3/3) (1/3) +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) (0/1) +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 (5/5) (5/5) (5/5) (1/5) +ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) (1/1) +rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) (1/1) +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads To update https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 0.8.0 rasusa 2.0.0 (0/1) (0/1) (1/1) (0/1) +raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. Up-to-date https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.3 raven-assembler 1.8.3 (0/1) (1/1) (1/1) (1/1) +raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) (1/1) +rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 (0/1) (0/1) (1/1) (0/1) +read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) (0/1) +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.14.0 recentrifuge 1.14.0 (0/1) (0/1) (1/1) (1/1) +red 578.0 88.0 red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) (1/1) +repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) (1/1) +repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib (1/1) (0/1) (0/1) (0/1) +reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 (2/2) (0/2) (2/2) (2/2) +resize_coordinate_window 85.0 5.0 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python (1/1) (0/1) (1/1) (0/1) +revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) +rgcca 44.0 3.0 rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 (1/1) (0/1) (1/1) (0/1) +rgrnastar 416677.0 3843.0 rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b (2/2) (2/2) (2/2) (2/2) +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) (0/2) +rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.2.3 rnaquast 2.2.3 (1/1) (0/1) (1/1) (1/1) +roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) +rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor (0/1) (0/1) (0/1) (0/1) +rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths (0/1) (0/1) (0/1) (0/1) +rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign (0/1) (0/1) (0/1) (0/1) +rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools (0/1) (0/1) (0/1) (0/1) +rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools (0/5) (0/5) (0/5) (0/5) +rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser (0/1) (0/1) (0/1) (0/1) +rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing Up-to-date https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.3 (22/22) (22/22) (22/22) (22/22) +ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) (0/1) +salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) (0/1) +samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) (0/1) +samtools To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.15.1 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.1 sansa 0.2.1 (0/1) (0/1) (1/1) (0/1) +sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) +sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) +sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol (0/1) (0/1) (0/1) (0/1) +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) (0/6) +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (5/5) (5/5) (0/5) +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 (1/1) (0/1) (1/1) (0/1) +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) (0/16) +scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) (0/1) +scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) (0/1) +scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) (0/1) +seacr 3693.0 50.0 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 (1/1) (0/1) (1/1) (0/1) +selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 (0/1) (0/1) (0/1) (0/1) +semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 (0/6) (0/6) (6/6) (1/6) +seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) (0/1) +seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) (0/1) +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis Up-to-date https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.8.2 seqkit 2.8.2 (0/5) (2/5) (3/5) (2/5) +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) +seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) (15/15) +seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.10 (0/1) (0/1) (1/1) (0/1) +seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) +shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.12.0 (0/1) (1/1) (1/1) (0/1) +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) +shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) +sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) (1/1) +simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 (0/4) (2/4) (4/4) (0/4) +sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) (0/1) +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.9.0 sinto 0.10.1 (2/2) (0/2) (2/2) (0/2) +slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) (0/2) +sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) (0/1) +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 (0/1) (0/1) (1/1) (0/1) +smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) (0/1) +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) (0/2) +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Epigenetics, Sequence Analysis snapatac2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.5.3 (0/4) (0/4) (4/4) (0/4) +sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 1.0.12 sniffles 2.3.3 (1/1) (1/1) (1/1) (1/1) +snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) (0/1) +snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) (3/3) +snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 (1/1) (1/1) (1/1) (0/1) +snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 (1/1) (1/1) (1/1) (0/1) +snpeff 101254.0 2843.0 snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 (5/5) (5/5) (5/5) (5/5) +snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 (1/1) (1/1) (1/1) (1/1) +snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base (1/1) (1/1) (1/1) (1/1) +snpsift 5109063.0 1185.0 snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 (8/8) (8/8) (8/8) (8/8) +snpsift_dbnsfp 46.0 11.0 snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +snpsift_genesets 390.0 11.0 snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) (0/1) +sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades coronaspades, biosyntheticspades, metaviralspades, metaspades, rnaspades, rnaviralspades, spades, plasmidspades, metaplasmidspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) +spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python (2/2) (0/2) (2/2) (0/2) +spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) +spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) +sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.1 sra-tools 3.1.1 (3/3) (3/3) (3/3) (3/3) +srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) (12/13) +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) (12/12) +star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 (1/1) (1/1) (1/1) (0/1) +straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 (0/3) (0/3) (0/3) (0/3) +strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 (2/2) (0/2) (2/2) (0/2) +stringtie 167659.0 2165.0 stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 (2/2) (2/2) (2/2) (2/2) +structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) (1/1) +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) (0/1) +swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 (0/1) (0/1) (0/1) (0/1) +syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) (0/1) +table_compute 208652.0 741.0 table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas (1/1) (1/1) (1/1) (1/1) +tabular_to_fastq 7388.0 200.0 tabular_to_fastq Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +tag_pileup_frequency 164.0 7.0 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk (1/1) (0/1) (1/1) (0/1) +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) (1/1) +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction Up-to-date https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 6.2.1 tb-profiler 6.2.1 (1/1) (1/1) (1/1) (0/1) +tb_variant_filter 19252.0 209.0 tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 (1/1) (1/1) (1/1) (0/1) +tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) (1/1) +tbvcfreport 2290.0 167.0 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1.0.0 tbvcfreport 1.0.0 (1/1) (1/1) (1/1) (0/1) +te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) (0/1) +tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) (0/1) +tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) (0/1) +tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.6 tn93 1.0.14 (4/4) (0/4) (4/4) (0/4) +tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. Data handling, Parsing Microbiology, Bioinformatics, Sequence analysis Up-to-date https://gitlab.com/ifb-elixirfr/abromics/tooldistillator Sequence Analysis tooldistillator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator 0.8.5.0 tooldistillator 0.8.5.0 (0/2) (0/2) (2/2) (2/2) +tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.3 tracegroomer 0.1.3 (0/1) (0/1) (1/1) (1/1) +tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) (0/4) +transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) (1/1) +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) +transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) +trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) (1/1) +trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) +trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) +tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.5 (0/1) (0/1) (1/1) (1/1) +tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) (1/1) +twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 377 ucsc-twobittofa 455 (1/1) (1/1) (1/1) (0/1) +tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) (0/1) +ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 377 ucsc-blat 445 (0/1) (0/1) (0/1) (0/1) +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.2 umi_tools 1.1.5 (5/5) (5/5) (5/5) (5/5) +unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) (1/1) +usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) (0/2) +valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 (1/1) (0/1) (1/1) (1/1) +vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) (0/1) +vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) (0/1) +variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) (0/3) +varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (3/3) (3/3) (3/3) +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.2.0 varvamp 1.2.0 (0/1) (0/1) (1/1) (0/1) +vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF To update Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.22 (0/1) (1/1) (1/1) (0/1) +vcf2tsv 167913.0 352.0 vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfaddinfo 357.0 8.0 vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfallelicprimitives 15803.0 286.0 vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 (0/1) (0/1) (1/1) (0/1) +vcfannotate 2181.0 77.0 vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfannotategenotypes 192.0 28.0 vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbedintersect 3217.0 80.0 vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbreakcreatemulti 471.0 13.0 vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcheck 675.0 39.0 vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcombine 1695.0 99.0 vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcommonsamples 244.0 14.0 vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfdistance 564.0 40.0 vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffilter 44444.0 882.0 vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffixup 917.0 71.0 vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfflatten 177.0 6.0 vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgeno2haplo 718.0 36.0 vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgenotypes 451.0 48.0 vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfhethom 1370.0 90.0 vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfleftalign 279.0 10.0 vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfprimers 708.0 12.0 vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfrandomsample 159.0 5.0 vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfselectsamples 854.0 29.0 vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfsort 1852.0 63.0 vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfvcfintersect 972774.0 265.0 vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3) +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 (1/1) (0/1) (1/1) (0/1) +velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) (2/2) +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) +verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.1 (0/1) (0/1) (1/1) (0/1) +vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.56.0 (0/3) (0/3) (3/3) (3/3) +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) +virheat virheat generates a heatmap of allele frequencies from vcf files virheat virheat Up-to-date https://github.com/jonas-fuchs/virHEAT Visualization, Variant Analysis virheat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat 0.7 virheat 0.7 (0/1) (0/1) (0/1) (0/1) +virhunter 234.0 40.0 virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) (1/1) +vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.28.1 (8/8) (8/8) (8/8) (8/8) +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 (0/5) (0/5) (0/5) (0/5) +weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) (0/1) +weblogo3 2370.0 74.0 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 (1/1) (1/1) (1/1) (1/1) +wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 447 ucsc-wigtobigwig 447 (1/1) (1/1) (1/1) (0/1) +windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) +winnowmap 248.0 27.0 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 (0/1) (0/1) (1/1) (0/1) +xpath 234.0 3.0 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) (0/1) +yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) (0/1) +zerone 90.0 2.0 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) (0/1) diff --git a/results/repositories04.list_tools.json b/results/repositories04.list_tools.json new file mode 100644 index 00000000..305b9ad3 --- /dev/null +++ b/results/repositories04.list_tools.json @@ -0,0 +1,7961 @@ +[ + { + "Galaxy wrapper id": "ThermoRawFileParser", + "Galaxy tool ids": [ + "thermo_raw_file_converter" + ], + "Description": "Thermo RAW file converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/compomics/ThermoRawFileParser", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "thermo_raw_file_converter", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": 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Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu -ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 (0/1) (1/1) (1/1) -appendfdr append_fdr To update appendfdr galaxyp 0.2.0 (0/1) (0/1) (0/1) -bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) -blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) -bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) -calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) -cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) -dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) -decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) -dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) -dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) -diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN 1.8.1 (0/1) (1/1) (1/1) -diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) -diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation Up-to-date https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.6 (0/1) (0/1) (1/1) -digestdb digestdb To update digestdb galaxyp 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) -directag_and_tagrecon To update directag_and_tagrecon galaxyp (0/1) (0/1) (0/1) -data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager (0/1) (0/1) (0/1) -data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) -eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (1/3) (3/3) (3/3) -encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) -fasta_merge_files_and_filter_unique_sequences 29886.0 461.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python (1/1) (1/1) (1/1) -fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) -feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) -filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) -flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) -gffcompare_to_bed 2115.0 131.0 gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python (1/1) (1/1) (1/1) -hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) -idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) -lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) -ltq_iquant_cli To update ltq_iquant_cli galaxyp (0/1) (0/1) (0/1) -maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant 1.22.0 r-base (0/2) (2/2) (2/2) -map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) -maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) -meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) -metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator 1.0.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) -metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) -metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) -mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp 1.0.0 mgf-formatter 1.0.0 (0/1) (0/1) (0/1) -moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) -morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 287 (0/1) (1/1) (1/1) -mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) -msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container To update Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) -msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2023.01.1202 (0/1) (0/1) (1/1) -msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) -msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) -msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) -mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse (0/1) (0/1) (1/1) -mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data To update Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) -openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (1/164) (36/164) (160/164) -pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) -pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) -pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) -pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) -peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp 1.0.0 python (1/1) (1/1) (1/1) -peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.5 (4/4) (4/4) (4/4) -pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) -percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator 3.5 percolator 3.5 (0/4) (4/4) (4/4) -pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) -pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) -custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) -custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db (0/1) (0/1) (0/1) -psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) -proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp 0.1 (0/5) (0/5) (0/5) -retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 (0/1) (0/1) (0/1) -translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) -proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) -proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) -proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) -proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) -proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) -proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) -proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) -proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python (0/1) (0/1) (0/1) -protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) -psm_eval psm_eval To update psm_eval galaxyp 0.1.0 binaries_for_psm_eval (0/1) (0/1) (0/1) -psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) -pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) -pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.6.3 (0/1) (0/1) (1/1) -quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) -quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) -qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter 0.1.0+galaxy1 geojson (0/1) (0/1) (1/1) -rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) -regex_find_replace 60307.0 495.0 regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python (2/2) (2/2) (2/2) -scaffold scaffold, scaffold_export To update scaffold galaxyp 0.1.0 scaffold (0/2) (0/2) (0/2) -sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) -spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) -spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) -translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) -unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs 4.5.1 python (1/1) (1/1) (1/1) -uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) -validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) -bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 (5/5) (4/5) (5/5) -biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.5.2 scipy (4/4) (0/4) (4/4) -ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 21.10 ambertools (7/7) (1/7) (7/7) -packmol 288.0 15.0 packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem 18.169.1 packmol (1/1) (0/1) (1/1) -topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python (2/2) (0/2) (2/2) -free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy (0/1) (0/1) (0/1) -gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 (12/15) (7/15) (15/15) -mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.0.0 mdanalysis (10/10) (1/10) (10/10) -mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter 1.9.7 mdtraj (1/1) (1/1) (1/1) -mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer 1.9.9 mdtraj (1/1) (1/1) (1/1) -mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ 1.9.7 mdtraj (1/1) (0/1) (1/1) -openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer (0/1) (0/1) (1/1) -vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd (0/1) (0/1) (0/1) -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.19.2 (0/1) (0/1) (0/1) -bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.0 (0/1) (0/1) (0/1) -bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) -bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 377 (0/1) (0/1) (0/1) -blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) -blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python (0/1) (0/1) (0/1) -blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) -blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) -cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) -cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python (0/1) (0/1) (0/1) -concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.2 (1/1) (1/1) (1/1) -cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.5.2 r-optparse 1.3.2 (0/1) (0/1) (0/1) -deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) -embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 (0/1) (0/1) (0/1) -fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 (0/1) (0/1) (0/1) -fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) -gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.4.0.0 (0/3) (0/3) (0/3) -get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 (0/1) (0/1) (0/1) -gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -gsc_scran_normalize 78.0 14.0 scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 (0/1) (0/1) (1/1) -gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) -high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils (0/1) (0/1) (0/1) -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz (0/1) (0/1) (0/1) -lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 (0/2) (0/2) (0/2) -manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta 1.6 samtools 1.19.2 (0/1) (0/1) (1/1) -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats 0.19.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.5.1 tar (0/1) (1/1) (0/1) -mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs To update http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns 3.4.0+galaxy2 bioconductor-mutationalpatterns 3.12.0 (0/1) (0/1) (0/1) -oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/oases 1.3.0 oases 0.2.09 (0/1) (0/1) (0/1) -pathifier 228.0 10.0 pathifier pathifier To update https:// Transcriptomics, Statistics pathifier artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier 1.0.2 r-optparse 1.3.2 (0/1) (0/1) (1/1) -pindel pindel Pindel detects genome-wide structural variation. To update http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel 0.2.5b8+galaxy1 pindel 0.2.5b9 (0/1) (0/1) (0/1) -probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage 0.7.0 samtools 1.19.2 (0/1) (0/1) (0/1) -repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/nskvir/RepEnrich Transcriptomics, Variant Analysis repenrich artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich 1.5.2 bioconductor-edger 4.0.2 (0/2) (2/2) (0/2) -rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) -sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba 0.7.1+galaxy1 sambamba 1.0 (0/1) (1/1) (0/1) -sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) -sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter 2.2.0 python (0/1) (0/1) (0/1) -small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters 1.3.0 pysam 0.22.0 (0/1) (0/1) (0/1) -small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) -small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures 3.4.2 pysam 0.22.0 (0/2) (0/2) (0/2) -snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 (0/2) (0/2) (0/2) -sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) -sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) -tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) -varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf 0.1 python (0/1) (0/1) (0/1) -xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) -yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) -EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) -Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/5) (0/5) (5/5) -Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) -PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy 0.0.2 (0/5) (5/5) (5/5) -ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 (0/1) (0/1) (1/1) -champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) -consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) -data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools 0.0.0 r-tangles (0/6) (0/6) (6/6) -xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ 2022.3.0 xarray (5/6) (2/6) (6/6) -gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) -interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) -obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) -ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) -regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) -spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) -srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) -stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc 0.0.2 (0/5) (0/5) (5/5) -vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) -xmlstarlet 14.0 4.0 xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet 1.6.1 xmlstarlet (0/1) (0/1) (1/1) -c3s 198.0 5.0 c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.1.0 python (1/1) (1/1) (1/1) -cads 52.0 1.0 cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python (0/1) (0/1) (1/1) -cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 (0/2) (0/2) (2/2) -cesm 13.0 1.0 cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM 2.1.3 cesm 2.1.3 (0/1) (0/1) (1/1) -climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) -eodie 45.0 4.0 eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE 1.0.2 eodie (0/1) (0/1) (1/1) -essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python (0/1) (0/1) (1/1) -fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald (1/1) (1/1) (1/1) -mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) -psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) -shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python (0/1) (0/1) (1/1) -smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python (0/1) (0/1) (0/1) -droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) -fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) -gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.0 (1/1) (1/1) (1/1) -fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 (0/1) (0/1) (0/1) -fastq_quality_trimmer 191.0 cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 (0/1) (0/1) (0/1) -fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) -salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) -cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) -data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) -data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) -decoupler score_genes_aucell, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.4.0+galaxy1 decoupler 1.5.0 (0/2) (0/2) (1/2) -dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) -garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) -monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) -sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) -scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy 1.8.1 scanpy-scripts 1.1.6 (17/27) (27/27) (27/27) -scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) -sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 (0/4) (0/4) (4/4) -sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.0.5 r-sceasy 0.0.7 (1/1) (0/1) (1/1) -scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.6.3 scmap-cli 0.1.0 (0/7) (0/7) (7/7) -scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) -seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.3.0 seurat-scripts 4.0.0 (0/13) (0/13) (12/13) -ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml 1.0.0+galaxy1 ucsc-cell-browser 1.2.3 (0/1) (0/1) (1/1) -biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) -filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.24.0 matchms 0.24.1 (2/13) (9/13) (13/13) -msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.3.0 msmetaenhancer 0.3.0 (0/1) (1/1) (1/1) -msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.24.1 (0/1) (0/1) (0/1) -mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) -query query Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click (0/1) (0/1) (0/1) -ramclustr 15.0 2.0 ramclustr, ramclustr_define_experiment ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 (2/2) (2/2) (2/2) -recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.12.0 r-recetox-aplcms 0.12.0 (0/8) (8/8) (8/8) -recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 (0/1) (0/1) (0/1) -recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 (0/1) (1/1) (1/1) -rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas (0/1) (0/1) (1/1) -retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 (0/4) (0/4) (0/4) -riassigner 15.0 3.0 riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.3.4 riassigner 0.3.4 (1/1) (0/1) (1/1) -rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python (0/1) (1/1) (1/1) -spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 (0/2) (0/2) (0/2) -waveica 6.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 (1/1) (0/1) (1/1) -xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb (0/1) (0/1) (1/1) -consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) -suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy (0/1) (0/1) (0/1) -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml 0.9.3 htslib 1.19.1 (4/4) (0/4) (4/4) -fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) -fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.12 (0/1) (0/1) (0/1) -getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) -hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) -incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) -measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) -omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) -omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) -omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) -omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20231220 fiji 20231211 (0/1) (0/1) (0/1) -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.19.2 (1/1) (0/1) (1/1) -upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) -blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) -blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) -blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) -make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) -ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) (9/9) +Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/6) (0/6) (6/6) (5/6) +Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) (3/3) +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 (0/5) (5/5) (5/5) (5/5) +ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.4 (0/1) (1/1) (1/1) (0/1) +ab1_fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files To update Convert Formats ab1fastq ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 1.20.0 bioconductor-sangerseqr 1.38.0 (0/1) (0/1) (1/1) (1/1) +ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools (7/7) (2/7) (7/7) (0/7) +appendfdr append_fdr To update appendfdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 (0/1) (0/1) (0/1) (0/1) +aquainfra_importer aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 1.0 (0/1) (0/1) (1/1) (0/1) +artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) (0/1) +bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) (0/1) +bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 377 (0/1) (0/1) (0/1) (0/1) +bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 (5/5) (4/5) (5/5) (0/5) +biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy (4/4) (0/4) (4/4) (0/4) +biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) (1/1) +blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) (0/1) +blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) (0/1) +blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python (0/1) (0/1) (0/1) (0/1) +blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python (0/1) (0/1) (0/1) (0/1) +blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 2.7.1 python (0/1) (0/1) (0/1) (0/1) +blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) (0/1) +blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) (0/1) +bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) (0/5) +c3s 198.0 5.0 c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.2.0 python (1/1) (1/1) (1/1) (0/1) +cads 52.0 1.0 cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python (0/1) (0/1) (1/1) (0/1) +calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) (0/1) +cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) (0/1) +cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) (11/11) +cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 (0/2) (0/2) (2/2) (0/2) +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) (0/8) +cesm 13.0 1.0 cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 2.1.3 cesm 2.1.3 (0/1) (0/1) (1/1) (0/1) +champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) (3/3) +cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content To update http://artbio.fr Fasta Manipulation cherry_pick_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 4.1 python (0/1) (0/1) (0/1) (0/1) +climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python (1/1) (1/1) (1/1) (0/1) +concat_multi_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. To update http://artbio.fr Text Manipulation concatenate_multiple_datasets artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1.4.2 (1/1) (1/1) (1/1) (0/1) +consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) (1/1) +consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.20 (4/5) (0/5) (5/5) (0/5) +cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.5.2 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) (1/1) +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager (0/1) (0/1) (0/1) (0/1) +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) (0/1) +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) (1/1) +data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles (0/6) (0/6) (6/6) (6/6) +data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper (0/1) (0/1) (0/1) (0/1) +data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) (0/1) +dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) (1/1) +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 (0/3) (0/3) (1/3) (0/3) +decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) (0/1) +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) (0/1) +dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) (0/1) +dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) (0/1) +diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 (0/1) (1/1) (1/1) (0/1) +diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) (0/1) +diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 (0/1) (0/1) (1/1) (0/1) +digestdb digestdb To update digestdb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +directag_and_tagrecon To update directag_and_tagrecon galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon (0/1) (0/1) (0/1) (0/1) +droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot 1.6.1+galaxy2 scxa-plots 0.0.1 (1/1) (0/1) (1/1) (0/1) +dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) (0/2) +eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (3/3) (3/3) (3/3) (3/3) +embl2fa embl2fa Converts EMBL flat format to fasta format To update http://artbio.fr Text Manipulation embl2fa artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa 0.2 (0/1) (0/1) (0/1) (0/1) +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) (0/7) +eodie 45.0 4.0 eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 1.0.2 eodie (0/1) (0/1) (1/1) (0/1) +essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python (0/1) (0/1) (1/1) (0/1) +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 (0/1) (0/1) (0/1) (0/1) +fasta_merge_files_and_filter_unique_sequences 29886.0 461.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python (1/1) (1/1) (1/1) (1/1) +fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) (0/2) +fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 (0/1) (0/1) (0/1) (0/1) +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 (0/1) (0/1) (0/1) (0/1) +fastq_quality_trimmer 191.0 cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 (0/1) (0/1) (0/1) (0/1) +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 (0/2) (0/2) (0/2) (0/2) +fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald (1/1) (1/1) (1/1) (0/1) +feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) (0/1) +fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers To update http://artbio.fr Fasta Manipulation, Data Source fetch_fasta_from_ncbi artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 3.1.0 urllib3 1.12 (0/1) (0/1) (0/1) (0/1) +filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) (1/1) +filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) (0/1) +flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) (0/1) +free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy (0/1) (0/1) (0/1) (0/1) +frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 (0/1) (0/1) (0/1) (0/1) +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) (0/7) +gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations To update http://artbio.fr Variant Analysis gatk4 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 (0/3) (0/3) (0/3) (0/3) +gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 (0/1) (0/1) (1/1) (0/1) +gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) (8/8) +getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +get_reference_fasta get_fasta_reference Obtain reference genome sequence. To update http://artbio.fr Data Source, Fasta Manipulation get_reference_fasta artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0.3.2 (0/1) (0/1) (0/1) (0/1) +gffcompare_to_bed 2115.0 131.0 gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python (1/1) (1/1) (1/1) (0/1) +gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. To update https://github.com/gromacs Molecular Dynamics, Computational chemistry gromacs chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 2022 gromacs 2021.3 (14/15) (8/15) (15/15) (0/15) +gsc_center_scale center_scale Center or scale (standardize) data To update http://artbio.fr Statistics gsc_center_scale artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gsc_scran_normalize 78.0 14.0 scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 (0/1) (0/1) (1/1) (0/1) +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 (1/1) (1/1) (1/1) (0/1) +guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) (0/1) +hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) (0/2) +high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) (0/1) +hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack To update Imaging hyperstack_to_bleach_corrected_movie lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 20230328 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) +idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) (0/1) +incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images to stack and upload to the omero server To update Imaging incucyte_stack_and_upload_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero 20231221 Fiji 20231211 (0/1) (0/1) (0/1) (0/1) +interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) (0/1) +isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 (0/1) (0/1) (1/1) (0/1) +justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils (0/1) (0/1) (0/1) (0/1) +justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz (0/1) (0/1) (0/1) (0/1) +lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) (0/1) +ltq_iquant_cli To update ltq_iquant_cli galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli (0/1) (0/1) (0/1) (0/1) +lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 (0/2) (0/2) (0/2) (0/2) +make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base (0/2) (2/2) (2/2) (2/2) +manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 1.6 manta 1.6.0 (0/1) (0/1) (1/1) (0/1) +map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 (0/1) (0/1) (0/1) (0/1) +matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.25.0 matchms 0.26.2 (2/14) (9/14) (13/14) (11/14) +maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) (0/2) +mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations To update https://github.com/MDAnalysis/mdanalysis Computational chemistry mdanalysis chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 1.0.0 mdanalysis (10/10) (1/10) (10/10) (0/10) +mdfileconverter md_converter A tool for interconverting between different MD structure and trajectory file formats. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1.9.7 mdtraj (1/1) (1/1) (1/1) (0/1) +mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To update Molecular Dynamics, Computational chemistry md_converter chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1.9.9 mdtraj (1/1) (1/1) (1/1) (0/1) +mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj (1/1) (0/1) (1/1) (0/1) +mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python (0/1) (0/1) (1/1) (0/1) +measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas (0/1) (0/1) (1/1) (0/1) +meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) (0/1) +metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) (0/1) +metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) (0/1) +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) (0/6) +mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 (0/1) (0/1) (0/1) (0/1) +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar (0/1) (1/1) (0/1) (0/1) +misc use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 (0/1) (0/1) (1/1) (0/1) +moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) (0/1) +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) (0/9) +morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 288 (0/1) (1/1) (1/1) (0/1) +mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) (0/2) +msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) (1/1) +msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 (0/1) (0/1) (1/1) (0/1) +msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 (0/1) (1/1) (1/1) (1/1) +msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) (1/1) +msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.26.2 (0/1) (0/1) (0/1) (0/1) +msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) (0/1) +msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) (0/1) +mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse (0/1) (0/1) (1/1) (0/1) +mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 (0/1) (0/1) (0/1) (0/1) +mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) (0/1) +mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) (0/1) +ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) (16/18) +oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 1.4.0 oases 0.2.09 (0/1) (0/1) (0/1) (0/1) +obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) (1/2) +ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) (0/1) +ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base (0/1) (0/1) (1/1) (0/1) +ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base (0/1) (0/1) (1/1) (0/1) +omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) +omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20231211 (0/1) (0/1) (0/1) (0/1) +openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer (0/1) (0/1) (1/1) (0/1) +openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (8/164) (35/164) (160/164) (0/164) +packmol 288.0 15.0 packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations To update http://m3g.iqm.unicamp.br/packmol/home.shtml Molecular Dynamics, Computational chemistry packmol chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 18.169.1 packmol (1/1) (0/1) (1/1) (0/1) +pathifier 228.0 10.0 pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 (0/1) (0/1) (1/1) (0/1) +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) (0/1) +pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) (0/1) +pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) (0/1) +pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) (0/3) +peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python (1/1) (1/1) (1/1) (0/1) +peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.9 (4/4) (4/4) (4/4) (4/4) +pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) (0/1) +percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator To update Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.6.5 (0/4) (4/4) (4/4) (0/4) +pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) (0/3) +pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 (0/1) (0/1) (0/1) (0/1) +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) (0/1) +positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 (0/5) (0/5) (0/5) (0/5) +proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python (0/1) (0/1) (0/1) (0/1) +protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) (1/1) +psm_eval psm_eval To update psm_eval galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval (0/1) (0/1) (0/1) (0/1) +psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) (0/1) +psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python (0/1) (0/1) (1/1) (0/1) +pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) (0/6) +pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.2 (0/1) (0/1) (1/1) (0/1) +qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 (0/3) (0/3) (3/3) (0/3) +quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) (1/1) +quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) (0/1) +query query Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click (0/1) (0/1) (0/1) (0/1) +qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.2.1 geojson (0/1) (0/1) (1/1) (0/1) +ramclustr 15.0 2.0 ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 (2/2) (2/2) (2/2) (2/2) +rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) (0/1) +recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.12.0 r-recetox-aplcms 0.12.0 (0/8) (8/8) (8/8) (8/8) +recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 (0/1) (0/1) (1/1) (1/1) +recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 (0/1) (1/1) (1/1) (1/1) +regex_find_replace 60307.0 495.0 regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python (2/2) (2/2) (2/2) (2/2) +regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) (7/7) +rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas (0/1) (0/1) (1/1) (0/1) +rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results To update https://github.com/RECETOX/galaxytools/ Metabolomics rename_annotated_feature recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 1.0.0 pandas (0/1) (0/1) (0/1) (0/1) +repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 (0/2) (2/2) (0/2) (0/2) +repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 (0/2) (0/2) (0/2) (0/2) +retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 (0/4) (0/4) (0/4) (0/4) +retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 (0/1) (0/1) (0/1) (0/1) +revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.20 (1/1) (0/1) (1/1) (0/1) +riassigner 15.0 3.0 riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.1 riassigner 0.4.1 (1/2) (0/2) (2/2) (1/2) +rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python (0/1) (1/1) (1/1) (1/1) +rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) (0/4) +salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 0.0.1+galaxy6 scipy (1/1) (1/1) (1/1) (0/1) +sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0.1 (0/1) (1/1) (0/1) (0/1) +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) (0/1) +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 (0/7) (0/7) (7/7) (0/7) +scaffold scaffold, scaffold_export To update scaffold galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold (0/2) (0/2) (0/2) (0/2) +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 (17/27) (27/27) (27/27) (0/27) +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 (0/6) (1/6) (6/6) (0/6) +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 (0/4) (0/4) (4/4) (0/4) +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 (1/1) (0/1) (1/1) (0/1) +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 (0/7) (0/7) (7/7) (0/7) +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) (0/4) +sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base (0/1) (0/1) (0/1) (0/1) +sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 2.2.0 python (0/1) (0/1) (0/1) (0/1) +seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (14/19) (11/19) +shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python (0/1) (0/1) (1/1) (0/1) +sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) (0/4) +small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 1.3.0 pysam 0.22.1 (0/1) (0/1) (0/1) (0/1) +small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 3.1.1 numpy (0/1) (0/1) (0/1) (0/1) +small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 3.4.2 pysam 0.22.1 (0/2) (0/2) (0/2) (0/2) +smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python (0/1) (0/1) (0/1) (0/1) +snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 (0/2) (0/2) (0/2) (0/2) +spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 (0/2) (0/2) (0/2) (0/2) +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) (1/1) +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie 2.3.0 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) +sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 (0/1) (0/1) (0/1) (0/1) +srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) (7/7) +stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 (0/5) (0/5) (5/5) (5/5) +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl (0/1) (0/1) (0/1) (0/1) +tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0.6.1 pigz (0/1) (0/1) (0/1) (0/1) +topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python (2/2) (0/2) (2/2) (0/2) +translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) (0/1) +translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.6 (0/1) (0/1) (1/1) (0/1) +unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python (1/1) (1/1) (1/1) (0/1) +uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) (0/1) +upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) +validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) (0/1) +varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. To update http://artbio.fr Variant Analysis varscan_vaf artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0.1 python (0/1) (0/1) (0/1) (0/1) +vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) +vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 (0/4) (0/4) (4/4) (4/4) +vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd (0/1) (0/1) (0/1) (0/1) +waveica 6.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 (1/1) (0/1) (1/1) (1/1) +xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray (5/6) (2/6) (6/6) (5/6) +xmlstarlet 14.0 4.0 xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 1.6.1 xmlstarlet (0/1) (0/1) (1/1) (1/1) +xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 2.1+galaxy0 xpore 2.1 (0/2) (0/2) (0/2) (0/2) +xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb (0/1) (0/1) (1/1) (1/1) +yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) (0/1) +zoo_project_ogc_api_processes zoo_project_ogc_api_processes This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes 0.1.0 r-base (0/1) (0/1) (1/1) (0/1) diff --git a/results/test.list_tools.tsv b/results/test.list_tools.tsv index afd5a69d..26ce4559 100644 --- a/results/test.list_tools.tsv +++ b/results/test.list_tools.tsv @@ -1,21 +1,5 @@ -Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version -Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests -GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ 0.3.1 -TreeBest treebest_best TreeBeST best To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2_ep78 -apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ 1.0+galaxy1 apoc 1b16 -blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 -ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 -export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ 0.0.2 EXPORT_DIR_PREFIX -gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b -gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python -hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 -hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 -lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.28.1 lotus2 2.30 -miranda miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a -plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 -rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ 1.0 rDock 2013.1 -replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ 0.1 python -rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 -smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 -smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ 1.0 smina 2017.11.9 -t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b +Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu +2d_auto_threshold 6541.0 39.0 ip_threshold Automatic thresholding scikit-image scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language To update https://github.com/bmcv Imaging 2d_auto_threshold imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold 0.0.6-2 scikit-image (0/1) (1/1) (1/1) +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (0/1) +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1)