From b28b3a07c07e0c4fafcceab1aed23f31aa057845 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 10 Jan 2024 10:58:32 +0100 Subject: [PATCH] Ci prod (#35) * action in main to manually dispatch * update * update * update * update * All tools bot * full wf * update * filter community tool bot * filter communities bot * test flter * filter communities bot * trigger pages only when new results are created * Update .github/workflows/static.yml Co-authored-by: Nicola Soranzo * fetch tools stepwise with CI * update CI * updat CI * update CI * update CI * update CI and get more verbose tool logs * add a test case to check what up with the CI * allow to run the test ever * try test with other api key * next try * as secrets * fetch all tools bot * merge test * cat in CI * CI all tools * CI test * force push * fetch all tools bot - step merge * test git merge * more tests * cover staged change as well * fetch all tools bot - step fetch * CI test * fetch all tools bot - step fetch * update fetch and filter CI * removed results from test runs * fetch all tools bot - step fetch * try pull merge with rebase * merge then push * test * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * CI update * fetch all tools bot - step fetch * fetch all tools bot - step merge * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step merge * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step merge * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step merge * fetch all tools bot - step fetch * fetch all tools bot - step merge * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step fetch * fetch all tools bot - step merge * Add nsoranzo review --------- Co-authored-by: github-actions Co-authored-by: Nicola Soranzo --- .github/workflows/fetch_all_tools.yaml | 75 + .github/workflows/filter_communities.yaml | 38 + .github/workflows/run_tests.yaml | 66 + .github/workflows/static.yml | 5 +- bin/extract_all_tools.sh | 0 bin/extract_all_tools_downstream.sh | 8 + bin/extract_all_tools_stepwise.sh | 12 + bin/extract_all_tools_test.sh | 13 + bin/extract_galaxy_tools.py | 46 +- bin/get_community_tools.sh | 0 results/all_tools.tsv | 518 +++---- results/imaging/index.html | 2 +- results/index.html | 1574 +++++++++++++-------- results/microgalaxy/index.html | 2 +- results/repositories01.list_tools.tsv | 153 ++ results/repositories02.list_tools.tsv | 331 +++++ results/repositories03.list_tools.tsv | 585 ++++++++ results/repositories04.list_tools.tsv | 262 ++++ results/test.list_tools.tsv | 21 + 19 files changed, 2883 insertions(+), 828 deletions(-) create mode 100644 .github/workflows/fetch_all_tools.yaml create mode 100644 .github/workflows/filter_communities.yaml create mode 100644 .github/workflows/run_tests.yaml mode change 100644 => 100755 bin/extract_all_tools.sh create mode 100644 bin/extract_all_tools_downstream.sh create mode 100755 bin/extract_all_tools_stepwise.sh create mode 100755 bin/extract_all_tools_test.sh mode change 100644 => 100755 bin/get_community_tools.sh create mode 100644 results/repositories01.list_tools.tsv create mode 100644 results/repositories02.list_tools.tsv create mode 100644 results/repositories03.list_tools.tsv create mode 100644 results/repositories04.list_tools.tsv create mode 100644 results/test.list_tools.tsv diff --git a/.github/workflows/fetch_all_tools.yaml b/.github/workflows/fetch_all_tools.yaml new file mode 100644 index 00000000..1293f272 --- /dev/null +++ b/.github/workflows/fetch_all_tools.yaml @@ -0,0 +1,75 @@ +name: Fetch all tools + +on: + workflow_dispatch: + schedule: + #Every Sunday at 8:00 am + - cron: "0 8 * * 0" + +# 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. +concurrency: + group: "tools" + cancel-in-progress: false + +permissions: + contents: write + +jobs: + fetch-all-tools-stepwise: + runs-on: ubuntu-20.04 + environment: fetch-tools + name: Fetch all tool stepwise + strategy: + matrix: + python-version: [3.8] + subset: + - repositories01.list + - repositories02.list + - repositories03.list + - repositories04.list + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install requirement + run: python -m pip install -r requirements.txt + - name: Run script + run: | + export GITHUB_API_KEY=${{ secrets.GH_API_TOKEN }} + bash ./bin/extract_all_tools_stepwise.sh "${{ matrix.subset }}" + - name: Commit all tools + # add or commit any changes in results if there was a change, merge with main and push as bot + run: | + git config user.name github-actions + git config user.email github-actions@github.com + git pull --no-rebase -s recursive -X ours + git add results + git status + git diff --quiet && git diff --staged --quiet || (git commit -m "fetch all tools bot - step fetch") + git push + + fetch-all-tools-merge: + runs-on: ubuntu-20.04 + needs: fetch-all-tools-stepwise + name: Fetch all tools merge + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + - name: Install requirement + run: python -m pip install -r requirements.txt + - name: Run script + run: | + cat results/repositories*.list_tools.tsv > results/all_tools.tsv + bash ./bin/extract_all_tools_downstream.sh + - name: Commit all tools + # add or commit any changes in results if there was a change, merge with main and push as bot + run: | + git config user.name github-actions + git config user.email github-actions@github.com + git pull --no-rebase -s recursive -X ours + 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 diff --git a/.github/workflows/filter_communities.yaml b/.github/workflows/filter_communities.yaml new file mode 100644 index 00000000..174a01f6 --- /dev/null +++ b/.github/workflows/filter_communities.yaml @@ -0,0 +1,38 @@ +name: Filter community tools + +on: + workflow_dispatch: + + # the workflow it triggered when all_tools_tsv is changed + push: + paths: + - 'results/all_tools_tsv' + 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. +concurrency: + group: "filter" + cancel-in-progress: false + +permissions: + contents: write + +jobs: + filter-all-tools: + runs-on: ubuntu-20.04 + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + - name: Install requirement + run: python -m pip install -r requirements.txt + - name: Run script + run: | + bash ./bin/get_community_tools.sh + - name: Commit results + # commit the new filtered data, only if stuff was changed + run: | + git config user.name github-actions + git config user.email github-actions@github.com + git diff --quiet || (git add results && git commit -m "filter communities bot") + git push diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml new file mode 100644 index 00000000..802a3b58 --- /dev/null +++ b/.github/workflows/run_tests.yaml @@ -0,0 +1,66 @@ +name: Run tests + +on: + workflow_dispatch: + +# 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. +# concurrency: +# group: "tools" +# cancel-in-progress: false + +permissions: + contents: write + +jobs: + fetch-all-tools-stepwise: + runs-on: ubuntu-20.04 + environment: fetch-tools + name: Fetch all tool stepwise + strategy: + matrix: + python-version: [3.8] + subset: + - test.list + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Install requirement + run: python -m pip install -r requirements.txt + - name: Run script + # run: bash bin/extract_all_tools.sh + run: | + export GITHUB_API_KEY=${{ secrets.GH_API_TOKEN }} + bash ./bin/extract_all_tools_test.sh "${{ matrix.subset }}" + - name: Commit all tools + # add or commit any changes in results if there was a change, merge with main and push as bot + run: | + git config user.name github-actions + git config user.email github-actions@github.com + git pull --no-rebase -s recursive -X ours + git add results + git status + git diff --quiet && git diff --staged --quiet || (git commit -m "fetch all tools bot - step fetch") + git push + + # fetch-all-tools-merge: + # runs-on: ubuntu-20.04 + # needs: fetch-all-tools-stepwise + # name: Fetch all tools merge + # steps: + # - uses: actions/checkout@v4 + # - uses: actions/setup-python@v5 + # - name: Install requirement + # run: python -m pip install -r requirements.txt + # - name: Run script + # run: | + # cat results/repositories*.list_tools.tsv > results/all_tools.tsv + # bash ./bin/extract_all_tools_downstream.sh + # - name: Commit all tools + # run: | + # git config user.name github-actions + # git config user.email github-actions@github.com + # git diff --quiet || (git add results && git commit -m "fetch all tools bot - step merge") + # git push \ No newline at end of file diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml index 63f26e63..b2907462 100644 --- a/.github/workflows/static.yml +++ b/.github/workflows/static.yml @@ -2,10 +2,13 @@ name: Deploy static content to Pages on: - # Runs on pushes targeting the default branch + # the workflow is triggered only when results are changed push: + paths: + - 'results' branches: ["main"] + # Allows you to run this workflow manually from the Actions tab workflow_dispatch: diff --git a/bin/extract_all_tools.sh b/bin/extract_all_tools.sh old mode 100644 new mode 100755 diff --git a/bin/extract_all_tools_downstream.sh b/bin/extract_all_tools_downstream.sh new file mode 100644 index 00000000..aca00afa --- /dev/null +++ b/bin/extract_all_tools_downstream.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env bash + +mkdir -p 'results/' + +python bin/create_interactive_table.py \ + --table "results/all_tools.tsv" \ + --template "data/interactive_table_template.html" \ + --output "results/index.html" \ No newline at end of file diff --git a/bin/extract_all_tools_stepwise.sh b/bin/extract_all_tools_stepwise.sh new file mode 100755 index 00000000..7b9cac75 --- /dev/null +++ b/bin/extract_all_tools_stepwise.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +mkdir -p 'results/' + +output="results/${1}_tools.tsv" + +python bin/extract_galaxy_tools.py \ + extractools \ + --api $GITHUB_API_KEY \ + --all_tools $output \ + --planemorepository $1 + diff --git a/bin/extract_all_tools_test.sh b/bin/extract_all_tools_test.sh new file mode 100755 index 00000000..9960b9ea --- /dev/null +++ b/bin/extract_all_tools_test.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +mkdir -p 'results/' + +output="results/${1}_tools.tsv" + +python bin/extract_galaxy_tools.py \ + extractools \ + --api $GITHUB_API_KEY \ + --all_tools $output \ + --planemorepository $1 \ + --test + diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py index b7eaf1b1..c17676cc 100644 --- a/bin/extract_galaxy_tools.py +++ b/bin/extract_galaxy_tools.py @@ -57,18 +57,36 @@ def get_string_content(cf: ContentFile) -> str: return base64.b64decode(cf.content).decode("utf-8") -def get_tool_github_repositories(g: Github) -> List[str]: +def get_tool_github_repositories(g: Github, RepoSelection: Optional[str], run_test: bool) -> 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 """ + + if run_test: + return ["https://github.com/TGAC/earlham-galaxytools"] + repo = g.get_user("galaxyproject").get_repo("planemo-monitor") repo_list: List[str] = [] for i in range(1, 5): - repo_f = repo.get_contents(f"repositories0{i}.list") - repo_l = get_string_content(repo_f).rstrip() - repo_list.extend(repo_l.split("\n")) + repo_selection = f"repositories0{i}.list" + if RepoSelection: # only get these repositories + if RepoSelection == repo_selection: + repo_f = repo.get_contents(repo_selection) + repo_l = get_string_content(repo_f).rstrip() + repo_list.extend(repo_l.split("\n")) + else: + repo_f = repo.get_contents(repo_selection) + repo_l = get_string_content(repo_f).rstrip() + repo_list.extend(repo_l.split("\n")) + + print("Parsing repositories from:") + for repo in repo_list: + print("\t", repo) + return repo_list @@ -475,11 +493,18 @@ 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", - "-o", - required=True, - help="Filepath to TSV with all extracted tools", + "--planemorepository", "-pr", required=False, help="Repository list to use from the planemo-monitor repository" + ) + + extractools.add_argument( + "--test", + "-t", + action="store_true", + default=False, + required=False, + help="Run a small test case using only the repository: https://github.com/TGAC/earlham-galaxytools", ) # Filter tools @@ -517,12 +542,11 @@ def filter_tools( # connect to GitHub g = Github(args.api) # get list of GitHub repositories to parse - repo_list = get_tool_github_repositories(g) - + 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 tools: List[Dict] = [] for r in repo_list: - print(r) + print("Parsing tools from:", (r)) if "github" not in r: continue try: diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh old mode 100644 new mode 100755 diff --git a/results/all_tools.tsv b/results/all_tools.tsv index 36c59e0e..61f3654a 100644 --- a/results/all_tools.tsv +++ b/results/all_tools.tsv @@ -1,8 +1,8 @@ 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 -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 3.56.2 +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 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 braker 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 -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 . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.3 +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 . 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 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 gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest 0.1.0 openjdk 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 @@ -14,7 +14,7 @@ openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard 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 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 Up-to-date 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.post0 +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 @@ -23,9 +23,9 @@ gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/ 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 2.23 lotus2 2.28 +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 2.30 lotus2 2.31 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 1.62.1 +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 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 @@ -45,7 +45,7 @@ combine_assembly_stats combine_stats Combine multiple Assemblystats datasets int combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml 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 cryptogenotyper 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 -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 0.28.0 +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 ectyper 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 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 fasta_extract 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 @@ -58,8 +58,8 @@ hivtrace hivtrace An application that identifies potential transmission clusters 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 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 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 -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 -mob_suite 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 3.1.7 +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.snapshot_2015_02_13 +mob_suite 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 mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml 1.0.2 mrbayes 3.2.7 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 pangolin 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 @@ -72,7 +72,7 @@ promer promer4_substitutions Aligns two sets of contigs and reports amino acid s 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 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 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 -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 +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 r82 sistr_cmd 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 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 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 @@ -83,11 +83,11 @@ staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml 1.1.0 stringMLST 0.6.3 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 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 -camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics 1.48.0 r-snow 0.4_1 +camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos To update Metabolomics camera workflow4metabolomics 1.48.0 r-snow 0.3_13 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 genform 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 -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/ 5.1.0 influx_si 7.0.1 -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 1.26.0 +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 +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 isoplot 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 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 mixmodel4repeated_measures 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 @@ -98,57 +98,60 @@ nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Prepr normalization 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 physiofit physiofit PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth rate during (batch) cultivations of microorganisms. Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment). Up-to-date Metabolomics physiofit workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit 2.2.1 physiofit4galaxy 2.2.1 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 -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 3.22.0 +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 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 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 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 -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 0.4.8 genoboo 0.4.8 +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 jbrowse 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 +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 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 w4mcorcov 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 w4mclassfilter 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 w4mjoinpn 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 -2d_auto_threshold ip_threshold Automatic thresholding 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 scikit-image -2d_feature_extraction ip_2d_feature_extraction 2D feature extraction 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 pandas -2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules 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 scikit-image -2d_histogram_equalization ip_histogram_equalization 2d histogram equalization 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 scikit-image -2d_simple_filter ip_filter_standard 2d simple filter 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 scikit-image -2d_split_binaryimage_by_watershed ip_2d_split_binaryimage_by_watershed split object by watershed To update https://github.com/bmcv Imaging 2d_split_binaryimage_by_watershed imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_split_binaryimage_by_watershed/ 0.0.1 scikit-image +2d_auto_threshold 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 +2d_feature_extraction 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 +2d_filter_segmentation_by_features 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 +2d_histogram_equalization 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 +2d_simple_filter 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 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 -anisotropic_diffusion 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 scikit-image -bfconvert 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+galaxy1 bftools 6.7.0 -binary2labelimage ip_binary_to_labelimage Binary 2 label image To update https://github.com/bmcv Imaging binary2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ 0.4 scikit-image -binaryimage2points ip_binaryimage_to_points Binary Image to Points To update https://github.com/bmcv Imaging binaryimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ 0.1 numpy -color-deconvolution ip_color_deconvolution Color-deconvolution methods To update https://github.com/bmcv Imaging color_deconvolution imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ 0.8 scikit-image -concat_channels ip_concat_channels Concatenate images To update https://github.com/bmcv Imaging concat_channels imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ 0.2 scikit-image -coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI 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 scikit-image -count_objects ip_count_objects Count Objects 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 scikit-image +anisotropic_diffusion 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 +bfconvert 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 +binary2labelimage 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 +binaryimage2points 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 +bioformats2raw 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 +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 +concat_channels 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 +coordinates_of_roi 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 +count_objects 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 curl_post 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 -curve_fitting ip_curve_fitting Polynomial curve fitting to data points 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 numpy -detection_viz ip_detection_viz Detection Visualization To update https://github.com/bmcv Imaging detection_viz imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ 0.3 scikit-image -image_info 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/ 0.2 bftools 6.7.0 -image_registration_affine ip_image_registration Intensity-based Image Registration 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 scikit-image -imagecoordinates_flipaxis imagecoordinates_flipaxis Flip coordinate axes To update https://github.com/bmcv Imaging imagecoordinates_flipaxis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ 0.1 pandas -labelimage2points ip_labelimage_to_points Label Image to Points To update https://github.com/bmcv Imaging labelimage2points imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ 0.2 scikit-image -landmark_registration ip_landmark_registration Landmark Registration 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 scikit-image -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 mahotas -mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Label Image To update https://github.com/bmcv Imaging mergeneighboursinlabelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage 0.3 scikit-image -overlay_images ip_overlay_images Overlay two images 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/ 0.0.3 scikit-image -permutate_axis ip_permutate_axis Permutates axes To update https://github.com/bmcv Imaging permutate_axis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ 0.2 scikit-image -points2binaryimage ip_points_to_binaryimage Points to Binary Image To update https://github.com/bmcv Imaging points2binaryimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ 0.2 scikit-image -points2labelimage ip_points_to_label Points to label image To update https://github.com/bmcv Imaging points2labelimage imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ 0.3 numpy -points_association_nn ip_points_association_nn Association of points in consecutive frames 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 numpy -projective_transformation ip_projective_transformation Projective transformation 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 scikit-image -projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates 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 scikit-image -scale_image ip_scale_image Scale image To update https://github.com/bmcv Imaging scale_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ 0.4 pillow -segmetrics ip_segmetrics Image segmentation and object detection performance measures To update https://github.com/bmcv Imaging segmetrics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ 1.4.0-1 segmetrics 1.4 -slice_image ip_slice_image Slice image To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3 scikit-image -split_labelmap ip_split_labelmap Split Labelmaps To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2 scikit-image -spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence 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 imageio -superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images 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 +curve_fitting 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 +detection_viz 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 +image_info 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 +image_registration_affine 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 +imagecoordinates_flipaxis 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 +labelimage2points 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 +landmark_registration 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 +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 +mergeneighboursinlabelimage 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 +overlay_images 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 +permutate_axis 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 +points2binaryimage 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 +points2labelimage 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 +points_association_nn 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 +projective_transformation 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 +projective_transformation_points 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 +rfove 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 +scale_image 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 +segmetrics 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 +slice_image 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 +split_labelmap 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 +spot_detection_2d 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 +superdsm 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 unzip 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 -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 visceral-evaluatesegmentation 2015.07.03 -wsi_extract_top_view 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 scikit-image +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 +wsi_extract_top_view 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 +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 add_value 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 annotation_profiler 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 best_regression_subsets 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 @@ -240,7 +243,7 @@ substitutions substitutions1 Fetch substitutions from pairwise alignments T t_test_two_samples 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 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 tabular_to_fasta 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 -tophat 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 1.18 +tophat 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 tophat2 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 2.5.2 tophat_fusion_post 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+ trimmer 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 @@ -279,7 +282,7 @@ t2ps Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/ t2t_report 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 vcftools_annotate 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 vcftools_compare 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 -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 1.18 +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 vcftools_isec 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 vcftools_merge 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 vcftools_slice 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 @@ -304,17 +307,18 @@ augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomi bamhash 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 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 bigwig_to_bedgraph 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 +biomodelsML biomodels_biomd0000001066 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 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 bismark 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 blobtoolkit 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 blockbuster 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 canu 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 -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 To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools -cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.1 -chipseeker 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 1.36.0 +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 +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.6 +chipseeker 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 circexplorer 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 -combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 0.3.0 python -compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 +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 +compare_humann2_output 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 cpat 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 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 diff 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 @@ -324,10 +328,10 @@ epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. fastq_info 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 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 find_subsequences bg_find_subsequences To update find_subsequences bgruening 0.3 biopython 1.70 -flye 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 2.9.2 +flye 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 footprint 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 format_cd_hit_output 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 -format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 +format_metaphlan2_output 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 gfastats 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 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 gotohscan 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 @@ -336,11 +340,12 @@ graphclust graphclust GraphClust can be used for structural clustering of RNA se 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 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 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 -hifiasm 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 0.19.7 hifiasm 0.19.7 +hifiasm 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 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 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 -graphicsmagick 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/ 1.3.31 graphicsmagick 1.3.26 -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. To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 +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 +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 +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 instagraal 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 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 itsx 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 @@ -348,18 +353,19 @@ jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update 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 lighter 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 mafft 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 +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 mcl 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 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 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 -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 1.26.0 +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 metilene 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 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 minced 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 -minipolish 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 Sequence assembly 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 +minipolish 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 mitohifi 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 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 music_deconvolution 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 -nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. To update https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.13.2 nanopolish 0.14.0 +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 netboxr 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 nextdenovo 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 nucleosome_prediction 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 @@ -379,13 +385,13 @@ plotly_regression_performance_plots plotly_regression_performance_plots performa protease_prediction 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 protein_properties 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 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 -racon racon 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 1.5.0 racon 1.5.0 +racon 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 repeat_masker 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 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 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 antarna 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 aresite2 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 -blockclust 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 1.1.0 blockclust 1.1.0 +blockclust 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 cmsearch_deoverlap 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 cmv 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 cofold 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 @@ -409,7 +415,8 @@ nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date paralyzer 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 pipmir 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 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 -rcas 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 1.26.0 +rbpbench 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 +rcas 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 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 remurna 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 ribotaper 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 @@ -421,7 +428,7 @@ rnalien RNAlien RNAlien unsupervized RNA family model construction To updat rnasnp 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 rnaz 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 selectsequencesfrommsa 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 -sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 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 +sortmerna 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 sshmm 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 targetfinder 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 trna_prediction 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 @@ -431,7 +438,7 @@ salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produ 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 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 segemehl 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 -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 1.0.10.0 +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 splitfasta 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 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 stress_ng 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 @@ -439,64 +446,65 @@ add_line_to_file add_line_to_file Adds a text line to the beginning or end of a column_arrange_by_header 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 join_files_on_column_fuzzy 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 split_file_on_column 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 -split_file_to_collection 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 0.5.0 python +split_file_to_collection 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 text_processing 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 tgsgapcloser 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 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 trim_galore 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 uniprot_rest_interface 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 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 -wtdbg 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, Mapping assembly, k-mer counting Sequence assembly, Computer science, Informatics 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 +wtdbg 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 align_back_trans 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 chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc 0.0.3 biopython 1.70 -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 1.18 +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 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 -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 1.18 -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 1.18 +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 +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 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 -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 0.0.6 galaxy_sequence_utils 1.1.5 -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 0.0.6 galaxy_sequence_utils 1.1.5 +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 +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 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 -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 0.1.4 galaxy_sequence_utils 1.1.5 +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 get_orfs_or_cdss 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 mummer 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 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 -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 0.0.9 +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 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 -sample_seqs 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 0.2.5 biopython 1.70 -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 1.18 -samtools_depth 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 1.18 -samtools_idxstats 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 1.18 +sample_seqs 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 +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 +samtools_depth 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 +samtools_idxstats 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 seq_composition 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 -seq_filter_by_id 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 0.2.7 biopython 1.70 -seq_filter_by_mapping 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 0.0.7 biopython 1.70 -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 0.0.4 biopython 1.70 -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 0.0.16 galaxy_sequence_utils 1.1.5 -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 0.0.9 galaxy_sequence_utils 1.1.5 -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 0.0.14 biopython 1.70 -venn_list 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 0.1.1 galaxy_sequence_utils 1.1.5 +seq_filter_by_id 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 +seq_filter_by_mapping 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 +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 +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 +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 +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 +venn_list 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 +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 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 abricate 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 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 -abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss ABySS De novo genome sequence assembler. Genome assembly, De-novo assembly 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 +abyss 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 adapter_removal 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 add_input_name_as_column 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 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 -aldex2 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 1.32.0 +aldex2 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 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 -amplican 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 1.22.1 +amplican 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 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 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." 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 -ancombc 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. Differential gene expression profiling 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 2.2.0 -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/ 0.7.5 anndata 0.6.22 -annotatemyids 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 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 3.17.0 bioconductor-org.hs.eg.db 3.17.0 +ancombc 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 +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 +annotatemyids 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 arriba 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 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 -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 1.2.3 +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 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 augustus 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 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 -bakta 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 Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.8.2 +bakta 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 1.9.1 bam_to_scidx 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 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 bandage 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 @@ -507,12 +515,12 @@ basil basil Breakpoint detection, including large insertions Up-to-date htt bax2bam 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 bayescan 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 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 -bcftools 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 1.18 +bcftools 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 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 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 -beagle 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 +beagle 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 4.1_03May16.862.jar 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 -bedtools 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 2.31.0 +bedtools 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 bellerophon 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 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 binning_refiner 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 @@ -526,15 +534,15 @@ blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To bowtie2 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 2.5.2 bracken 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 To update https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken 2.8 bracken 2.9 breseq 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 0.38.1 -busco 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 5.4.6 busco 5.5.0 +busco 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 Up-to-date https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.5.0 bwa 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 bwa_mem2 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 bwameth 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 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 calculate_numeric_param 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 -cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) Up-to-date https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat 5.2.3 cat 5.2.3 +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 cdhit 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 -cemitool 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 1.24.0 +cemitool 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 charts 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 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 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 @@ -544,12 +552,12 @@ chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date h circexplorer2 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 circos 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 cite_seq_count 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 -clair3 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 1.0.4 +clair3 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 clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins " - clustalw + 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 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 -codeml 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 4.10.6 +codeml 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 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 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 collection_column_join 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 @@ -559,16 +567,16 @@ column_order_header_sort column_order_header_sort Sort Column Order by heading column_remove_by_header 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 compose_text_param 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 compress_file 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 -concoct 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. 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 +concoct 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 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 coverm coverm_contig, coverm_genome CoverM genome and contig wrappers 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 0.6.1 coverm 0.6.1 crispr_studio 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 crosscontamination_barcode_filter 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 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 0.6.5 -cutadapt 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 To update https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt 4.4 cutadapt 4.5 -cutesv 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 2.0.3 +cutadapt 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 +cutesv 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 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 -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 1.28.0 +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 das_tool 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 Up-to-date 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 1.1.6 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 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 @@ -578,24 +586,24 @@ deepmicro deepmicro Representation learning and classification framework " " Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 deepsig 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 deepvariant 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 -deg_annotate 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 2.31.0 -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 1.1.8 -deseq2 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 1.40.2 -dexseq 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 1.46.0 -diamond 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. 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 -diffbind 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+galaxy0 bioconductor-diffbind 3.10.0 +deg_annotate 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 +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 +deseq2 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 +dexseq 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 +diamond 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 +diffbind 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 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. Up-to-date https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet 0.1.4 dimet 0.1.4 disco 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 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 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 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 -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 To update https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.3 drep 3.4.5 -dropletutils 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 1.20.0 +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 +dropletutils 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 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 -edger 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 3.42.4 +edger 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 egsea 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 emboss_5 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 -ena_upload 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 0.6.3 ena-upload-cli 0.6.3 +ena_upload 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 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 ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions Up-to-date 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 110.1 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 @@ -607,14 +615,16 @@ fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fasta_nucleotide_color_plot 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 fasta_stats 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 fastani 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 -fastp fastp Fast all-in-one preprocessing for FASTQ files 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 +fastp 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 fastqc 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 fastqe 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 0.2.6+galaxy2 fastqe 0.3.1 fasttree 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 featurecounts 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 feelnc 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 -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 -fgsea 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 1.26.0 +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. To update https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit r193 fermi2 r188 +fgsea 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 filtlong 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 @@ -623,7 +633,7 @@ flash flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired- fraggenescan 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 freebayes 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 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 -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 1.4.7 +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 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 funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " funannotate @@ -637,9 +647,9 @@ genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis ut geneiobio 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 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 genomescope 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 -genomic_super_signature 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 1.8.0 +genomic_super_signature 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 genrich 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 -get_hrun 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 0.7.2.1 +get_hrun 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 0.7.2.2 getorganelle 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 gfa_to_fa 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 gff3_rebase 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 @@ -649,7 +659,7 @@ ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_ 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 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 goenrichment 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 -goseq 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 1.52.0 +goseq 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 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 graphembed 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 graphlan 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 @@ -657,51 +667,51 @@ gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective 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 gubbins 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 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 -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 1.46.0 +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 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 -hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation 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 +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 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 -hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes Up-to-date 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 1.3.6 +hapog 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 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 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 -heinz 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 1.60.0 -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. Up-to-date https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer 3.7.2 hicexplorer 3.7.2 +heinz 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 +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 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 -hifiasm_meta 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 +hifiasm_meta 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 hamtv0.1 hisat2 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 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 -hmmer3 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 Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 3.3.2 hmmer 3.3.2 +hmmer3 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 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 -htseq_count 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 2.0.3 +htseq_count 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 2.0.4 humann 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 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 -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 2.5.50 +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 2.5.58 hypo 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 icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Firmicutes genomes. 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 Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.2.0 icescreen 1.2.0 idba_ud 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 idr 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 -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 omero-py 5.11.1 +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 iedb_api 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 -instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/MrOlm/inStrain 1.5.3 instrain 1.8.0 -integron_finder 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 3.3.2 +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 +integron_finder 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 intermine_galaxy_exchange 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 -interproscan 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 +interproscan 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 5.52_86.0 interval2maf 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 intervene 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 -iqtree 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 2.2.5 -irissv 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 1.18 -isescan 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 -isoformswitchanalyzer 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 2.0.1 +iqtree 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 +irissv 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 +isescan 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 Up-to-date https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan 1.7.2.3 isescan 1.7.2.3 +isoformswitchanalyzer 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 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 -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 1.24.0 +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 jasminesv 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 jbrowse 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 -jcvi_gff_stats 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 1.3.8 +jcvi_gff_stats 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 jellyfish 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 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 jq 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 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 -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 0.50.0 +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 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 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 king 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 @@ -712,12 +722,12 @@ kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from kraken_taxonomy_report 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 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 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 -last 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 1454 +last 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 1522 lastz 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 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 legsta 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 length_and_gc_content 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 -limma_voom 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 3.56.2 +limma_voom 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 lineagespot 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 links 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 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 @@ -727,7 +737,7 @@ m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m maaslin2 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 macs2 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 maf_stats 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 -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 +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 maker 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 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 map_param_value 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 0.1.1 @@ -735,8 +745,8 @@ mapseq mapseq fast and accurate sequence read classification tool designed to as mash 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 masigpro 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 maxbin2 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 -mcl 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 To update https://micans.org/mcl/man/mcl.html mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl 14.137 mcl 22.282 -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 1.11.1 +mcl 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 +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 megahit 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 megahit_contig2fastg 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 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 @@ -745,30 +755,30 @@ meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clus 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 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 merqury 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 -meryl meryl Meryl a k-mer counter. 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 -metabat2 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. 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 -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 -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 1.42.0 +meryl 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 +metabat2 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 +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 1.ea903e5 +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 metaphlan 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 migmap 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 minia 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 -miniasm 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 +miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) Up-to-date https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm 0.3_r179 miniasm 0.3_r179 minimap2 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 miniprot 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 mirnature 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 mitobim 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 -mitos 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 1.1.1 mitos 2.1.3 +mitos 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 1.1.1 mitos 2.1.5 mlst 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 -moabs 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 -mosdepth 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 0.3.4 mosdepth 0.3.5 -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 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 +moabs 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 1.3.9.6 +mosdepth 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 +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 msaboot 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 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 -multigsea 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 1.10.0 -multiqc 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 1.17 +multigsea 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 +multiqc 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 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 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 -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 To update http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ 3.6.0 mzmine 3.9.0 +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 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 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 nanoplot 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 @@ -786,9 +796,9 @@ nonpareil nonpareil Estimate average coverage in metagenomic datasets To up novoplasty 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 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 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 -ococo ococo Variant detection of SNVs To update 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 0.1.2.4 +ococo ococo Variant detection of SNVs To update 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 0.1.2.7 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 0.8.3 -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 4.1.1 +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 3.1.3 ont-fast5-api 4.1.2 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 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 optitype 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 @@ -797,9 +807,9 @@ orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups 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 pangolin 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 parse_mito_blast 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 -pathview 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 1.40.0 +pathview 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 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 -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 1.13.0 +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 pe_histogram 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 pear 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 pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " @@ -807,9 +817,10 @@ pharokka pharokka rapid standardised annotation tool for bacteriophage genomes a " 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 " -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 1.44.0 +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 phyml 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 -picard 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 3.1.0 +picard 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 +pick_value 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 0.1.0 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 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 pilon 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 @@ -817,7 +828,7 @@ pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/ pizzly 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 plasflow 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 plasmidfinder 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 -plink 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 +plink 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 To update 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 1.90b6.12 polypolish 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 Up-to-date 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 0.5.0 porechop 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 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 @@ -826,8 +837,8 @@ pretext pretext_map, pretext_snapshot Process genome contacts maps processing im prinseq 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 progressivemauve 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 prokka 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 -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 0.1.4 prot-scriber 0.1.4 -proteinortho 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 To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.2.3 proteinortho 6.3.0 +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 +proteinortho 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 To update https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho 6.2.3 proteinortho 6.3.1 psiclass 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 pureclip 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 purge_dups 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 @@ -839,22 +850,22 @@ qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt F 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 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 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 -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 Up-to-date 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 2.2.2d +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 quast 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 query_impc 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 query_tabular 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 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 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 ragtag 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 -rapidnj 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 +rapidnj rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny To update https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj v2.3.2 raven 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 raxml 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 rcorrector 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 read_it_and_keep 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 -recentrifuge 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 1.12.1 recentrifuge 1.12.1 +recentrifuge 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 To update https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.12.1 recentrifuge 1.13.0 red 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 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 -repeatmodeler 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 2.0.4 +repeatmodeler 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 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 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 resize_coordinate_window 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 @@ -864,32 +875,34 @@ ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offset rnaquast 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 roary 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 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 -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 1.5.0 rp2paths +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 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 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 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 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 rseqc 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 -ruvseq 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 1.34.0 +ruvseq 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 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 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 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 sarscov2formatter 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 sarscov2summary 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 sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc 0.1.13 sbml2sbol -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/ @galaxy_version@ scanpy 1.7.2 -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 1.28.0 +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 +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 +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 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 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 scoary 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 -scpipe 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 2.0.0 +scpipe 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 seacr 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 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 -semibin 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, Visualisation 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 1.5.1 semibin 2.0.2 +semibin 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 seq2hla 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 seqcomplexity 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 -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 2.5.1 -seqtk 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_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 To update https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.3 seqtk 1.4 +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 +seqsero2 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 +seqtk 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 To update https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.4 seqtk r82 seqwish 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 seurat 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 shasta 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 @@ -905,7 +918,7 @@ smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manip smudgeplot 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 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 sniffles 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 -snipit snipit Summarise snps relative to a reference sequence To update https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit 1.0.7 snipit 1.1.2 +snipit snipit Summarise snps relative to a reference sequence To update https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit 1.0.7 snipit 1.2 snippy 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 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 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 @@ -917,8 +930,8 @@ spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, spaln 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 spotyping 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 spyboat 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 -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 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 3.0.8 sra-tools 3.0.8 -srst2 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 1.18 +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 +srst2 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 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 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 star_fusion 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 @@ -938,47 +951,48 @@ tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer tb_variant_filter 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 tbl2gff3 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 tbvcfreport 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 -te_finder 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 1.18 +te_finder 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 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 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 tetyper 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 -tn93 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 1.0.9 -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 0.7.5 +tn93 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 1.0.12 +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 transdecoder 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 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 transtermhp 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 -trinity 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 +trinity 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 To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity date.2011_11_26 trinotate 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 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 -tsebra tsebra This tool has been developed to combine BRAKER predictions. Up-to-date 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 +tsebra 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 tsne 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 -tximport 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 1.28.0 +tximport 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 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 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 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 -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 447 +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 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 unicycler 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 -usher 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 0.6.2 +usher 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 valet 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 vapor 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 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 variant_analyzer 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 varscan 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 vcf2maf 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 -vcfanno vcfanno Annotate VCF files 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/ 0.3.3 vcfanno 0.3.3 -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 +vcfanno 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 +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_2 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 velvet 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 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 verkko 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 -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 1.52.0 +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 1.53.0 virhunter 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 volcanoplot 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 -vsearch 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 2.24.0 +vsearch 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 2.26.1 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 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 weblogo3 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 +windowmasker 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 winnowmap 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 xpath 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 yahs 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 @@ -1025,7 +1039,7 @@ fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter Up-to-date http tabular_to_fastq 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 kraken 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 kraken2 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 -samtools To update SAM iuc 1.15.1 samtools 1.18 +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 snpeff 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 snpsift 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 snpsift_dbnsfp 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 @@ -1053,17 +1067,18 @@ vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To u vcfselectsamples 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 vcfsort 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 vcfvcfintersect 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 +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 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 appendfdr append_fdr To update appendfdr galaxyp 0.2.0 bed_to_protein_map 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 -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 2.14.1 -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 +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 +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_10158 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 -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 3.2.1 +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 dbbuilder 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 decoyfasta Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta dia_umpire 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 -dialignr 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 2.8.0 +dialignr 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 diann 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 diapysef 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 diffacto 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 @@ -1077,11 +1092,11 @@ fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_uniqu fastg2protlib 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 feature_alignment 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 filter_by_fasta_ids 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 -flashlfq 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 1.2.5 +flashlfq 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 gffcompare_to_bed 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 hardklor hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 idconvert 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 -lfq_protein_quant 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 2.26.0 +lfq_protein_quant 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 ltq_iquant_cli To update ltq_iquant_cli galaxyp 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 map_peptides_to_bed 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 @@ -1093,12 +1108,12 @@ metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquan mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp 1.0.0 mgf-formatter 1.0.0 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 morpheus 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 -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 1.62.1 +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 msconvert 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 msgfplus msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2023.01.1202 msms_extractor 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 -msstats 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 4.8.3 -msstatstmt 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 2.8.0 +msstats 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 +msstatstmt 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 mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse mz_to_sqlite 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 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 @@ -1107,7 +1122,7 @@ pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordin pepquery 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 pepquery2 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 peptide_genomic_coordinate 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 -peptideshaker 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 4.3.1 +peptideshaker 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 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 percolator 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 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 @@ -1132,7 +1147,7 @@ protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp 0.1.0 tr psm_eval psm_eval To update psm_eval galaxyp 0.1.0 binaries_for_psm_eval psm_validation 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 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 -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 4.6.2 +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 quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 quantwiz_iq 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 qupath_roi_splitter 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 @@ -1146,7 +1161,7 @@ translate_bed_sequences translate_bed_sequences Perform 3 frame translation of B unipept 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 uniprotxml_downloader 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 validate_fasta_database 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 -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 +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 2.2_3 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 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 packmol 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 @@ -1155,11 +1170,11 @@ free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Co 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 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 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 -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 1.9.7 mdtraj +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 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 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 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 -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 1.18 +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 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 bigwig_to_bedgraph 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 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 @@ -1171,35 +1186,35 @@ cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio http 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 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 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 -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 1.40.2 +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 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 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 -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 2.32.0 +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 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 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 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 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 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 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 -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/master/tools/gsc_high_dimension_visualization 0.9.6 r-optparse 1.3.2 -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/master/tools/gsc_mannwhitney_de 0.9.4 r-optparse 1.3.2 -gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize 0.2.1 r-optparse 1.3.2 -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/master/tools/gsc_signature_score 0.9.1 r-optparse 1.3.2 -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/master/tools/guppy 0.2.1 -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/master/tools/high_dim_heatmap 1.2.0 r-gplots 2.17.0 -justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/justdiff 0.6.0 -justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip 0.2 +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 +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 +gsc_scran_normalize 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 +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 +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 +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 +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 +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 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/master/tools/lumpy_smoove 0.2.8+galaxy0 svtyper 0.7.1 lumpy_sv lumpy Find structural variations To update http://artbio.fr Variant Analysis lumpy_sv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv 1.2.2 lumpy-sv 0.3.1 -manta 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 1.18 +manta 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 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 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 -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 3.10.0 +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 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 pathifier 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 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 -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 1.18 -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 3.42.4 +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 +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 rsem 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 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 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 @@ -1214,16 +1229,18 @@ tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To upda 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 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 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 -EMLassemblyline eml2eal, makeeml 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 0.1.0+galaxy0 r-emlassemblyline +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 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 +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 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 -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 1.36.0 +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 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 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 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 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 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 obisindicators obisindicators Compute biodiveristy indicators for marine data from obis To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base +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 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 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 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 @@ -1252,7 +1269,7 @@ salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix an 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 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 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 -decoupler 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+galaxy2 decoupler 1.5.0 +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 dropletutils 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 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 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 @@ -1261,21 +1278,22 @@ scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluste 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 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 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 -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 0.0.11 +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 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 seurat 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 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 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 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 -matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_networking, matchms_spectral_similarity, matchms_split 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 Up-to-date https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.23.1 matchms 0.23.1 +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 Up-to-date https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.24.0 matchms 0.24.0 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 0.3.0 msmetaenhancer 0.3.0 -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 0.23.1 +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 0.24.0 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 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 ramclustr 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 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 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 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 +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 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 riassigner 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 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 @@ -1293,15 +1311,21 @@ snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://sn 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 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 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 -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 1.18 +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 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 -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+galaxy0 gffutils 0.12 +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 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 -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 20220414 -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 20230824 Fiji 20220414 -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 20220414 -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 20220414 -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 20220414 -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 20230728 fiji 20220414 -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 1.18 +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 +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 +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 +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 +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 +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 +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 +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 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 +blast2go 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 +blast_rbh 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 +blastxml_to_top_descr 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 +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 +ncbi_blast_plus 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 diff --git a/results/imaging/index.html b/results/imaging/index.html index 857452ce..2c510f04 100644 --- a/results/imaging/index.html +++ b/results/imaging/index.html @@ -23,7 +23,7 @@ background-color: #00FFFF; color: #000000; min-width: 400px; - } + }