diff --git a/bin/create_interactive_table.py b/bin/create_interactive_table.py new file mode 100644 index 00000000..17711c23 --- /dev/null +++ b/bin/create_interactive_table.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python + +import argparse + +import pandas as pd + +# TODO maybe allow comunities to modify +COLUMNS = [ + "Expand", + "Galaxy wrapper id", + "Galaxy wrapper version", + "Conda version", + "Conda id", + "Status", + "bio.tool id", + "bio.tool name", + "EDAM operation", + "EDAM topic", + "Description", + "bio.tool description", + "Status", + "Source", + "ToolShed categories", + "ToolShed id", + "Galaxy wrapper owner", + "Galaxy wrapper source", +] + + +def generate_table( + tsv_path: str, + template_path: str, + output_path: str, +) -> None: + df = pd.read_csv(tsv_path, sep="\t").assign(Expand=lambda df: "").fillna("") + df = df[df["To keep"]].loc[:, COLUMNS].reindex(columns=COLUMNS) + table = df.to_html(border=0, table_id="dataframe", classes=["display", "nowrap"], index=False) + + with open(template_path) as template_file: + template = template_file.read() + + final_html_output = template.replace("COMMUNITY_TABLE", table) + + with open(output_path, "w") as output: + output.write(final_html_output) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Create interactive table from \ + TSV file using a template, where COMMUNITY_TABLE is replaced \ + by the rendered table" + ) + parser.add_argument( + "--table", + "-ta", + required=True, + help="Path to TSV file with tools", + ) + parser.add_argument( + "--template", + "-te", + required=True, + help="Path to HTML template", + ) + parser.add_argument( + "--output", + "-out", + required=True, + help="Path to HTML output", + ) + + args = parser.parse_args() + generate_table(args.table, args.template, args.output) diff --git a/bin/filter_microgalaxy_tools.sh b/bin/get_microgalaxy_tools.sh similarity index 74% rename from bin/filter_microgalaxy_tools.sh rename to bin/get_microgalaxy_tools.sh index b3613fd6..b8684d5b 100644 --- a/bin/filter_microgalaxy_tools.sh +++ b/bin/get_microgalaxy_tools.sh @@ -18,4 +18,9 @@ python bin/extract_galaxy_tools.py \ --filtered_tools 'results/microgalaxy/tools.tsv' \ --categories "data/microgalaxy/categories" \ --exclude "data/microgalaxy/tools_to_exclude" \ - --keep "data/microgalaxy/tools_to_keep" \ No newline at end of file + --keep "data/microgalaxy/tools_to_keep" + +python bin/create_interactive_table.py \ + --table 'results/microgalaxy/tools.tsv' \ + --template 'data/interactive_table_template.html' \ + --output 'results/microgalaxy/index.html' diff --git a/data/datatable_template.html b/data/datatable_template.html new file mode 100644 index 00000000..6e03634a --- /dev/null +++ b/data/datatable_template.html @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + +
+ +COMMUNITY_TABLE + +
\ No newline at end of file diff --git a/data/interactive_table_template.html b/data/interactive_table_template.html new file mode 100644 index 00000000..6e03634a --- /dev/null +++ b/data/interactive_table_template.html @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + +
+ +COMMUNITY_TABLE + +
\ No newline at end of file diff --git a/data/microgalaxy/tools_to_exclude b/data/microgalaxy/tools_to_exclude index d451b4a0..6f30553a 100644 --- a/data/microgalaxy/tools_to_exclude +++ b/data/microgalaxy/tools_to_exclude @@ -139,6 +139,7 @@ inforna intarna kinwalker locarna +mea mqc nastiseq paralyzer diff --git a/data/microgalaxy/tools_to_keep b/data/microgalaxy/tools_to_keep index 96cfbdfe..0e2d8278 100644 --- a/data/microgalaxy/tools_to_keep +++ b/data/microgalaxy/tools_to_keep @@ -47,7 +47,6 @@ nucleosome_prediction pfamscan racon infernal -mea rRNA reago sortmerna diff --git a/results/all_tools.tsv b/results/all_tools.tsv new file mode 100644 index 00000000..36c59e0e --- /dev/null +++ b/results/all_tools.tsv @@ -0,0 +1,1307 @@ +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 +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 +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 +helixer helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 +meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 +miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl +openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest 0.1.0 openjdk +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 +apoc apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ 1.0+galaxy1 apoc 1b16 +blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 +ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 +export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ 0.0.2 EXPORT_DIR_PREFIX +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b +gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python +hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 +hcluster_sg_parser hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 +lotus2 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection Metagenomics To update http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.23 lotus2 2.28 +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 +rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ 1.0 rDock 2013.1 +replace_chromosome_names replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ 0.1 python +rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 +smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ 1.0 smina 2017.11.9 +t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas 1.1 mummer 3.23 +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 +biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data to a Bionumerics friendly form To update https://github.com/phac-nml/galaxy_tools Text Manipulation biohansel_bionumeric_converter nml 0.2.0 pandas +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml 1.3.0 perl-getopt-long 2.54 +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml 5.1.0 gawk +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml 0.1 +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.54 +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 +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 +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml 0.1.4.1 srst2 0.2.0 +gnali gnali A tool to find nonessential, loss-of-function gene variants Up-to-date https://github.com/phac-nml/gnali/ Variant Analysis gnali nml https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace 1.0.1 hivtrace 1.5.0 +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 +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 +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist 0.1.2 python +plasmid_profiler plasmid_profiler Explores plasmid content in WGS data To update plasmid_profiler nml 0.1.6 r +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml 1.1 spades 3.15.5 +pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads Up-to-date https://github.com/phe-bioinformatics/PneumoCaT Variant Analysis pneumocat nml https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer 1.2 python +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 +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 +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml 1.0.1 spolpred +srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 +staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 +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 +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 +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 +ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. To update http://workflow4metabolomics.org Metabolomics ms2snoop workflow4metabolomics 2.2.1 r-base +nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation To update http://workflow4metabolomics.org Metabolomics nmr_annotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation 3.0.0 r-batch 1.1_4 +nmr_annotation2d 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra To update http://workflow4metabolomics.org Metabolomics 2dnmrannotation marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics 2.0.0 r-batch 1.1_4 +nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction To update http://workflow4metabolomics.org Metabolomics nmr_preprocessing marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing r-batch 1.1_4 +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 +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 +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 +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 +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 +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 +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 +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 +blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 1.0.0 +blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping 1.0.0 +bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. To update http://bowtie-bio.sourceforge.net/ Next Gen Mappers bowtie_wrappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers 1.2.0 bowtie 1.3.1 +canonical_correlation_analysis cca1 Canonical Correlation Analysis To update Statistics canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis 1.0.0 R +categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. To update Statistics categorize_elements_satisfying_criteria devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria 1.0.0 +ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool To update ChIP-seq ccat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat 0.0.2 ccat 3.0 +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 +change_case ChangeCase Convert column case. To update Text Manipulation change_case devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case 1.0.1 perl +compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs 1.0.0 +compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency 1.0.0 +compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values To update Statistics compute_q_values devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values 1.0.1 R +condense_characters Condense characters1 Condense consecutive characters. To update Text Manipulation condense_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters 1.0.0 +convert_characters Convert characters1 Convert delimiters to tab. To update Text Manipulation convert_characters devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters 1.0.1 python +convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides To update Fasta Manipulation convert_solid_color2nuc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc 1.0.0 +correlation cor2 Correlation for numeric columns To update Statistics correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation 1.0.0 rpy +count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 +ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch 1.0.0 +cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund 2.16.0 fonts-conda-ecosystem +cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. To update Convert Formats, Next Gen Mappers cummerbund_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular 1.0.1 +cut_columns Cut1 Select columns from a dataset. To update Text Manipulation cut_columns devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns 1.0.2 +delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels 1.0.0 +dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) To update Systems Biology, Variant Analysis dgidb_annotator devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator 0.1 +divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp 1.0.0 +draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria To update Graphics, Statistics draw_stacked_barplots devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots 1.0.0 R +dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences To update Statistics dwt_cor_ava_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass 1.0.1 r-waveslim 1.7.5 +dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features To update Statistics dwt_cor_avb_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all 1.0.1 r-waveslim 1.7.5 +dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences To update Statistics dwt_ivc_all devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all 1.0.1 r-waveslim 1.7.5 +dwt_var_perclass compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom Compute P-values and Max Variances for Feature Occurrences To update Statistics dwt_var_perclass devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass 1.0.1 r-waveslim 1.7.5 +dwt_var_perfeature dwt_var1 Wavelet variance using Discrete Wavelet Transfoms To update Statistics dwt_var_perfeature devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature 1.0.2 r-bitops +express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express 1.1.1 eXpress 1.5.1 +fasta_compute_length fasta_compute_length Compute sequence length To update Fasta Manipulation fasta_compute_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.3 python +fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species To update Fasta Manipulation fasta_concatenate_by_species devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species 0.0.1 bx-python 0.10.0 +fasta_filter_by_length fasta_filter_by_length Filter sequences by length To update Fasta Manipulation fasta_filter_by_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length 1.2 python +fasta_to_tabular fasta2tab FASTA-to-Tabular converter To update Fasta Manipulation fasta_to_tabular devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular 1.1.1 python +fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window Up-to-date Fastq Manipulation fastq_trimmer_by_quality devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 +fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data To update Convert Formats, Fastq Manipulation fastqsolexa_to_fasta_qual devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual 1.0.0 +featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter 2.0.0 bx-python 0.10.0 +filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking 0.1 +generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix 1.0.0 +getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way 1.0.0 bx-python 0.10.0 +getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 1.0.0 numpy +gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj 2.0.1 +hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat 1.0.3 hisat +histogram histogram_rpy Histogram of a numeric column To update Graphics, Statistics histogram devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 1.0.4 rpy2 2.7.8 +indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way 1.0.3 +kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis To update Statistics kernel_canonical_correlation_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis 1.0.0 rpy +kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis To update Statistics kernel_principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis 1.0.0 rpy +lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads To update Next Gen Mappers lastz_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads 1.1.1 lastz 1.04.22 +lda_analysis lda_analy1 Perform Linear Discriminant Analysis To update Graphics, Statistics lda_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis 1.0.1 R +linear_regression LinearRegression1 Perform Linear Regression To update Statistics linear_regression devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression 1.0.1 R +logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif 1.0.1 numpy +maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 1.0.0 bx-python 0.10.0 +mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc 1.0.0 +megablast_xml_parser megablast_xml_parser Parse blast XML output To update Next Gen Mappers, Convert Formats megablast_xml_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser 1.0.1 python +merge_cols mergeCols1 Merge columns together. To update Text Manipulation merge_cols devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols 1.0.3 python +microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath 1.0.0 +microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level 1.0.0 sputnik +microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability 1.1.0 bx-python 0.10.0 +mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration To update Variant Analysis mine devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine 0.0.1 MINE +multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik +mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs To update Variant Analysis mutate_snp_codon devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon 1.0.0 +partialr_square partialRsq Compute partial R square To update Statistics partialr_square devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square 1.0.0 R +pearson_correlation Pearson_and_apos_Correlation1 Pearson and apos Correlation between any two numeric columns To update Statistics pearson_correlation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation 1.0.0 +pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp To update Variant Analysis pgsnp2gd_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp 1.0.0 +pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases To update SAM pileup_interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval 1.0.3 bx-python 0.10.0 +pileup_parser pileup_parser Filter pileup on coverage and SNPs To update https://github.com/galaxyproject/tools-devteam/ SAM pileup_parser devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser 1.0.2 perl +plot_from_lda plot_for_lda_output1 "Draw ROC plot on ""Perform LDA"" output" To update Graphics, Statistics plot_from_lda devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda 1.0.1 R +principal_component_analysis pca1 Principal Component Analysis To update Statistics principal_component_analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis 1.0.2 rpy +quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 1.0.1 bx-python 0.10.0 +rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve 1.0.0 R +remove_beginning Remove beginning1 Remove lines from the beginning of a file. To update Text Manipulation remove_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning 1.0.0 +rmap rmap_wrapper RMAP for Solexa Short Reads Alignment To update Next Gen Mappers rmap devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap 1.0.0 rmap 2.1 +rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores To update Next Gen Mappers rmapq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq 1.0.0 rmap 2.1 +sam2interval sam2interval Convert SAM to interval. To update SAM sam2interval devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval 1.0.2 python +sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values To update SAM sam_bitwise_flag_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter 1.0.1 python +scatterplot scatterplot_rpy Scatterplot of two numeric columns To update Graphics, Statistics scatterplot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot 1.0.3 numpy +short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length 1.0.0 rpy +short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score 1.0.2 fontconfig +short_reads_trim_seq trim_reads Select high quality segments To update Fastq Manipulation short_reads_trim_seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq 1.0.0 +show_beginning Show beginning1 Select lines from the beginning of a file. To update Text Manipulation show_beginning devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning 1.0.0 +show_tail Show tail1 Select lines from the end of a file. To update Text Manipulation show_tail devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail 1.0.0 +sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions Up-to-date https://home.gwu.edu/~wpeng/Software.htm ChIP-seq sicer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer 1.1 SICER 1.1 +split_paired_reads split_paired_reads Split paired end reads To update Fastq Manipulation split_paired_reads devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads 1.0.0 +substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 1.0.0 +substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 1.0.1 bx-python 0.10.0 +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 +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 +ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python +varscan_version_2 varscan VarScan wrapper To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan_version_2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 2.4.2 varscan 2.4.6 +vcf2pgsnp vcf2pgSnp VCF to pgSnp To update Variant Analysis vcf2pgsnp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp 1.0.0 +vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) To update Variant Analysis vcf_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate 1.0.0 +vcf_extract vcf_extract Extract reads from a specified region To update Variant Analysis vcf_extract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract 1.0.0 +vcf_filter vcf_filter Filter a VCF file To update Variant Analysis vcf_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter 1.0.0 +vcf_intersect vcf_intersect Generate the intersection of two VCF files To update Variant Analysis vcf_intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect 1.0.0 +weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 +windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 +xy_plot XY_Plot_1 Plotting tool for multiple series and graph types To update Graphics, Statistics xy_plot devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot 1.0.2 r-base +basecoverage gops_basecoverage_1 Base Coverage of all intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations basecoverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage 1.0.0 bx-python 0.10.0 +cluster gops_cluster_1 Cluster the intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations cluster devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster 1.0.0 bx-python 0.10.0 +complement gops_complement_1 Complement intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations complement devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement 1.0.0 bx-python 0.10.0 +concat gops_concat_1 Concatenate two bed files To update https://github.com/galaxyproject/gops Genomic Interval Operations concat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat 1.0.1 bx-python 0.10.0 +coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals To update https://github.com/galaxyproject/gops Genomic Interval Operations coverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage 1.0.0 bx-python 0.10.0 +flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval To update https://github.com/galaxyproject/gops Genomic Interval Operations flanking_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features 4.0.1 bx-python 0.10.0 +get_flanks get_flanks1 Get flanks returns flanking region/s for every gene To update https://github.com/galaxyproject/gops Genomic Interval Operations get_flanks devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks 1.0.0 bx-python 0.10.0 +intersect gops_intersect_1 Intersect the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations intersect devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect 1.0.0 bx-python 0.10.0 +join gops_join_1 Join the intervals of two datasets side-by-side To update https://github.com/galaxyproject/gops Genomic Interval Operations join devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join 1.0.0 bx-python 0.10.0 +merge gops_merge_1 Merge the overlapping intervals of a dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge 1.0.0 bx-python 0.10.0 +subtract gops_subtract_1 Subtract the intervals of two datasets To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract 1.0.0 bx-python 0.10.0 +subtract_query subtract_query1 Subtract Whole Dataset from another dataset To update https://github.com/galaxyproject/gops Genomic Interval Operations subtract_query devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query 0.1 bx-python 0.10.0 +tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables To update https://github.com/galaxyproject/gops Genomic Interval Operations tables_arithmetic_operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations 1.0.0 perl +hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 +hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R +snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data To update Variant Analysis, Statistics snpfreq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq 1.0.1 R +find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 +gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 +kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk +lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 +poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 +t2ps Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 +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_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 +vcftools_subset vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 +10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust 0.5 graphclust-wrappers 0.6.0 +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 +agat agat GTF/GFF analysis toolkit agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics Up-to-date https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.2.0 +antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 +atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters 0.1.6 atactk 0.1.9 +augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 +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 +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 +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 +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 +diffbind Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind +edta edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta edta 2.1.0 +epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 +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 +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 +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 +graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 +graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust +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 +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 +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 +jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 +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 +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 +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 +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 +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 +numeric_clustering numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 +pandas_rolling_window pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy +peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 +perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf +pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 +pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools postgresql +pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat +piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus +plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas +plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python +plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python +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 +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 +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 +compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ 1.0 compalignp 1.0 +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 +dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python +dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 +dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 +infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs Up-to-date http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal 1.1.4 infernal 1.1.4 +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna +intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.3.2 intarna 3.3.2 +kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 +mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 +mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 +nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 +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 +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 +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ +rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 +rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 +rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender 0.1.1 sam 3.5 +rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 +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 +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 +vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 +sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.2 +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 +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 +add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 +barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 +basil basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc 1.2.0 anise_basil 1.2.0 +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 +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 +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 +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 +bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! To update https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ 0.20.4 python-bioext 0.21.2 +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 +biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 +blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast 1.7.0 magicblast 1.7.0 +blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 +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 +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 +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 +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 +chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 +chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 1.0.7 chopin2 +chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a +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 +clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins " + clustalw + " 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 +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 +collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers 0.0.2 +column_maker Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.0 python +column_order_header_sort column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python +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 +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 +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 +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 +decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator 1.0.0 numpy +deepmicro deepmicro Representation learning and classification framework " + DeepMicro + " Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 +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 +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 +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 +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 +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 +exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 +exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 +export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 +extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.10.0 +fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 +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 +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 +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 +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 +flash flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 +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 +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 + " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 +gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 4.1.7.0 gatk4 4.4.0.0 +gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy 1.0.0 python +gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko 1.2 gecko 1.2 +gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini 0.20.1 gemini 0.30.2 +genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 +genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ 3.0.0 ghm 3.1 +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 +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 +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 +gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare 0.12.6 gffcompare 0.12.6 +gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base +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 +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 +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 +kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma 1.2.21 kma 1.4.9 +kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 +kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 +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 +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 +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 +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 +lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv 0.3.1 lumpy-sv 0.3.1 +m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet 2.1.0 m6anet 2.1.0 +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 +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 +mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq 2.1.1 perl +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 +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 +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_fimo meme_fimo A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. Sequence motif discovery, Nucleic acid feature detection, Protein feature detection, Statistical calculation Sequence analysis, Genetic variation, Statistics and probability, Data mining To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme 5.4.1 meme 5.5.4 +meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 +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 +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 +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 +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 +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 +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 +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 +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 +ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 +ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets 15.19.1 ncbi-datasets-cli +ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases Up-to-date http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct 16.2 entrez-direct 16.2 +ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils 1.70 python +necat necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 +newick_utils newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 +nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 +ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr 0.2.7 ngmlr 0.2.7 +ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils ngsutils 0.5.9 +nonpareil nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 +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 +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 +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 +orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder 2.5.4 orthofinder 2.5.5 +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 +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 +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 " + pharokka + " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " + pharokka + " +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 +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 +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 +pipelign pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign 0.2 pipelign 0.2 +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 +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 +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto 0.6.2 presto 0.7.1 +pretext pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext 0.1.9 pretextmap 0.1.9 +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 +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 +pycoqc pycoqc QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc 2.5.2 pycoqc 2.5.2 +pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 5.0.2 pyega3 5.1.0 +pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks 3.8 pygenometracks 3.8 +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb 1.4.2 pysradb 2.2.0 +qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 +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 +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 +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 +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 +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 +rgcca rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca 3.0.2 rgccacmd 3.0.3 +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar 2.7.10b star 2.7.11a +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology Up-to-date https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz 1.2.0 ribowaltz 1.2.0 +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 +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 +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 +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 +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 +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 +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 +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah 1.1.3 shorah 1.99.2 +shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 +sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 +simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext 0.0.2 r-argparse 1.0.1 +sina sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto 0.9.0 sinto 0.10.0 +slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk 0.4.3 slamdunk 0.4.3 +sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 +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 +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 +snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff +snpfreqplot snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ 1.0 r-base +socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru 2.1.7 socru 2.2.4 +sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 +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 +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 +straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model Up-to-date https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.2 +strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka 2.9.10 strelka 2.9.10 +stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie 2.2.1 stringtie 2.2.1 +structure structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester 0.6.94 structureharvester 0.6.94 +swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ 1.0 swiftlink 1.0 +syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA 1.0 clustalo 1.2.4 +table_compute table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas +tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency 1.0.2 openjdk +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc 0.3.0 rust-ncbitaxonomy 1.0.7 +taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler 4.4.1 tb-profiler 5.0.1 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +zerone zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone 1.0 zerone 1.0 +bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 +bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 +bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 +cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 +cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 +cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 +cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 +cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 +cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 +fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 +fasta_formatter cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 +fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 +fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 +fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 +fastq_quality_filter cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 +fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 +fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 +fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 +fastx_clipper cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 +fastx_collapser cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 +fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 +fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 +fastx_renamer cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 +fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 +fastx_trimmer cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 +fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_filter fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_groomer fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_stats fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 +fastq_trimmer fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 +fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 +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 +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 +snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ snpsift 5.2 +vcf2tsv vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 +vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 +vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 +vcfannotate vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate vcflib 1.0.9 +vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 +vcfbedintersect vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 +vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 +vcfcheck vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck vcflib 1.0.9 +vcfcombine vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine vcflib 1.0.9 +vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 +vcfdistance vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance vcflib 1.0.9 +vcffilter vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter vcflib 1.0.9 +vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup vcflib 1.0.9 +vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten vcflib 1.0.9 +vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 +vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 +vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom vcflib 1.0.9 +vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign vcflib 1.0.9 +vcfprimers vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers vcflib 1.0.9 +vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 +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 +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 +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 +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 +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 +digestdb digestdb To update digestdb galaxyp 0.1.0 trans_proteomic_pipeline +directag_and_tagrecon To update directag_and_tagrecon galaxyp +data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager +data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath +eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 +fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python +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 +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 +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 +maxquant maxquant, maxquant_mqpar wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 +meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 +metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator 1.0.0 metagene_annotator 1.0 +metanovo metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 +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 +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 +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 +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 +pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python +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 +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 +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base +custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam 1.3.2.1 r-base +proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp 0.1 +retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 +translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 +proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 +proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 +proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 +proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 +proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 +proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 +proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 +proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 +proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 +proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python +protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp 0.1.0 trans_proteomic_pipeline +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 +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 +rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 +regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python +scaffold scaffold, scaffold_export To update scaffold galaxyp 0.1.0 scaffold +sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 +translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 +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 +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 +topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. To update https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors Molecular Dynamics, Computational chemistry topologyeditors chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python +free_energy Free energy tools of BRIDGE. To update Molecular Dynamics, Computational chemistry freeenergy chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy +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 +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 +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 +blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python +blast_unmatched blast_unmatched Extract unmatched query sequences from blast To update http://artbio.fr Fasta Manipulation blast_unmatched artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 1.0.1 python +blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits 2.7.1 python +blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python +cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 +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 +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 +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 +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 +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 +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 +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 +sequence_format_converter sequence_format_converter various fasta to tabular conversions To update http://artbio.fr Convert Formats, Fasta Manipulation sequence_format_converter artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter 2.2.0 python +small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters 1.3.0 pysam 0.22.0 +small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps 3.1.1 numpy +small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures 3.4.2 pysam 0.22.0 +snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza To update http://artbio.fr Variant Analysis snvtocnv artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv 3.0.0+galaxy1 sequenza-utils 3.0.0 +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie 2.3.0 bowtie 1.3.1 +sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 +tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 0.6.1 pigz +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 +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 +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 +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 +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 +stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc 0.0.2 +vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 +xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another To update Convert Formats xmlstarlet ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet 1.6.1 xmlstarlet +c3s c3s Copernicus Climate Change Service (C3S) To update https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset Climate Analysis c3s climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 0.1.0 python +cads cads Copernicus Atmosphere Data Store (ADS) To update https://ads.atmosphere.copernicus.eu/#!/home Climate Analysis cads climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0.1.0 python +cdo cdo_info, cdo_operations CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. To update https://code.mpimet.mpg.de/projects/cdo/ Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo 2.0.0 +cesm cesm Community Earth System Model (CESM) Up-to-date https://www.cesm.ucar.edu/ Climate Analysis cesm climate https://github.com/ESCOMP/CESM 2.1.3 cesm 2.1.3 +climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python +eodie eodie Earth Observation Data Information Extractor To update https://eodie.readthedocs.io/ Climate Analysis eodie climate https://gitlab.com/eetun-tiimi/EODIE 1.0.2 eodie +essential_climate_variables cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability To update https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview Climate Analysis, Data Source cds_essential_variability climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0.2.0 python +fates-emerald ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model To update https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api Climate Analysis ctsm_fates climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 2.0 fates-emerald +mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python +psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python +shift-longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ Climate Analysis shift_longitudes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0.1.0 python +smithsonian-volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database To update https://volcano.si.edu/gvp_votw.cfm Retrieve Data smithsonian_volcanoes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0.1.0 python +droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml 1.6.1+galaxy2 scxa-plots 0.0.1 +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 +gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.0 +fastq_pair fastq_pair Paired-end fastq pairer To update https://github.com/linsalrob/fastq-pair Fastq Manipulation fastq_pair ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair 1.0+galaxy0 fastq-pair 1.0 +fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality To update https://github.com/agordon/fastx_toolkit Fastq Manipulation fastq_quality_trimmer ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer 0.0.14+galaxy0 fastx_toolkit 0.0.14 +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 +salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml 0.0.1+galaxy6 scipy +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 +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 +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.8.0 sc3-scripts 0.0.6 +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy 1.8.1 scanpy-scripts 1.1.6 +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 +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 +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 +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 +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 +spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 +waveica waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 +xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb +consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. Up-to-date https://snvphyl.readthedocs.io/en/latest/ Variant Analysis positions2snv_invariant_alignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 +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 +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 +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 +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 diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html new file mode 100644 index 00000000..ae0ad294 --- /dev/null +++ b/results/microgalaxy/index.html @@ -0,0 +1,4443 @@ + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExpandGalaxy wrapper idGalaxy wrapper versionConda versionConda idStatusbio.tool idbio.tool nameEDAM operationEDAM topicDescriptionbio.tool descriptionStatusSourceToolShed categoriesToolShed idGalaxy wrapper ownerGalaxy wrapper source
TreeBest1.9.2.post01.9.2.post0treebestUp-to-dateTreeBeST bestUp-to-datehttp://treesoft.sourceforge.net/treebest.shtmlPhylogeneticstreebest_bestearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest
ete3.1.23.1.1ete3To updateAnalyse phylogenetic trees using the ETE ToolkitTo updatehttp://etetoolkit.org/Phylogeneticseteearlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete
lotus22.232.28lotus2To updatelotus2lotus2Sequence feature detectionMetagenomicsLotuS2 OTU processing pipelineLotuS2 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.To updatehttp://lotus2.earlham.ac.uk/Metagenomicslotus2earlhaminsthttps://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2
abacas1.13.23mummerTo updateOrder and Orientate ContigsTo updatehttps://github.com/phac-nml/abacasAssemblyabacasnmlhttps://github.com/phac-nml/abacas
assemblystats1.1.01.7.8perl-bioperlTo updateSummarise an assembly (e.g. N50 metrics)To updatehttps://github.com/phac-nml/galaxy_toolsAssemblyassemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
biohansel2.4.02.6.1bio_hanselTo updateHeidelberg and Enteritidis SNP ElucidationTo updatehttps://github.com/phac-nml/biohanselSequence Analysisbiohanselnmlhttps://github.com/phac-nml/biohansel
combine_assembly_stats1.02.54perl-getopt-longTo updateCombine multiple Assemblystats datasets into a single tabular reportTo updatehttps://github.com/phac-nml/galaxy_toolsAssemblycombine_assemblystatsnmlhttps://github.com/phac-nml/galaxy_tools
cryptogenotyper1.01.0cryptogenotyperUp-to-dateCryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.Up-to-datehttps://github.com/phac-nml/CryptoGenotyperSequence Analysiscryptogenotypernmlhttps://github.com/phac-nml/CryptoGenotyper
ectyper1.0.01.0.0ectyperUp-to-dateEC-Typer - in silico serotyping of Escherichia coli speciesUp-to-datehttps://github.com/phac-nml/ecoli_serotypingSequence Analysisectypernmlhttps://github.com/phac-nml/ecoli_serotyping
filter_spades_repeats1.0.11.7.8perl-bioperlTo updateRemove short and repeat contigs/scaffoldsTo updatehttps://github.com/phac-nml/galaxy_tools/Assemblyfilter_spades_repeatsnmlhttps://github.com/phac-nml/galaxy_tools/
getmlst0.1.4.10.2.0srst2To updateDownload MLST datasets by species from pubmlst.orgTo updateSequence Analysisgetmlstnml
hivtrace1.0.11.5.0hivtraceTo updateAn application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.To updateSequence Analysishivtracenmlhttps://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace
kat_filter2.32.4.2katTo updateFiltering kmers or reads from a database of kmers hashesTo updateSequence Analysiskat_filternml
mob_suite3.0.33.1.7mob_suiteTo updateMOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assembliesTo updatehttps://github.com/phac-nml/mob-suiteSequence Analysismob_suitenmlhttps://github.com/phac-nml/mob-suite
mrbayes1.0.23.2.7mrbayesTo updateA program for the Bayesian estimation of phylogeny.To updateSequence Analysismrbayesnml
mykrobe_parser0.1.4.1r-baseTo updateRScript to parse the results of mykrobe predictor.To updatehttps://github.com/phac-nml/mykrobe-parserSequence Analysismykrobe_parsernmlhttps://github.com/phac-nml/mykrobe-parser
plasmidspades1.13.15.5spadesTo updateGenome assembler for assemblying plasmidTo updateAssemblyplasmidspadesnml
promer1.2pythonTo updateAligns two sets of contigs and reports amino acid substitutions between themTo updatehttps://github.com/phac-nml/promerAssemblypromernmlhttps://github.com/phac-nml/promer
sistr_cmd1.1.11.1.1sistr_cmdUp-to-dateSISTR in silico serotyping toolUp-to-datehttps://github.com/phac-nml/sistr_cmdSequence Analysissistr_cmdnml
smalt0.7.60.7.6smaltUp-to-dateSMALT aligns DNA sequencing reads with a reference genome.Up-to-datehttp://www.sanger.ac.uk/science/tools/smalt-0Sequence Analysissmaltnmlhttps://sourceforge.net/projects/smalt/
srst20.3.70.2.0srst2To updateShort Read Sequence Typing for Bacterial PathogensTo updateSequence Analysissrst2nml
staramr0.10.00.10.0staramrUp-to-dateScan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.Up-to-datehttps://github.com/phac-nml/staramrSequence Analysisstaramrnmlhttps://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr
stringmlst1.1.00.6.3stringMLSTTo updateRapid and accurate identification of the sequence type (ST)To updateSequence Analysisstringmlstnml
cd_hit_dup0.0.14.8.1cd-hit-auxtoolsTo updatesimple tool for removing duplicates from sequencing readsTo updateMetagenomics, Sequence Analysiscd_hit_dupdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup
multispecies_orthologous_microsats1.0.0bx-sputnikTo updateExtract orthologous microsatellitesTo updateSequence Analysis, Variant Analysismultispecies_orthologous_microsatsdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats
quality_filter1.0.10.10.0bx-pythonTo updateFilter nucleotides based on quality scoresTo updateSequence Analysis, Variant Analysisquality_filterdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter
gi2taxonomy1.1.10.9.0taxonomyTo updateFetch taxonomic representationTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicsgi2taxonomydevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy
kraken2tax1.2+galaxy0gawkTo updateConvert Kraken output to Galaxy taxonomy data.To updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicskraken2taxdevteamhttps://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/
lca_wrapper1.0.10.9.0taxonomyTo updateFind lowest diagnostic rankTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicslca_wrapperdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper
t2ps1.0.00.9.0taxonomyTo updateDraw phylogenyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2psdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps
t2t_report1.0.00.9.0taxonomyTo updateSummarize taxonomyTo updatehttps://bitbucket.org/natefoo/taxonomyMetagenomicst2t_reportdevteamhttps://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report
antismash6.1.16.1.1antismashUp-to-dateantismashantiSMASHSequence clustering, Gene prediction, Differential gene expression analysisMolecular interactions, pathways and networks, Gene and protein familiesAntismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clustersRapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.Up-to-datehttps://antismash.secondarymetabolites.orgSequence Analysisantismashbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash
combine_metaphlan_humann0.3.0pythonTo updateCombine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundancesTo updateMetagenomicscombine_metaphlan2_humann2bebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2
compare_humann2_output0.2.0To updateCompare outputs of HUMAnN2 for several samples and extract similar and specific informationTo updateMetagenomicscompare_humann2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output
flye2.9.12.9.2flyeTo updateAssembly of long and error-prone reads.To updatehttps://github.com/fenderglass/Flye/Assemblyflyebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/flye
format_metaphlan2_output0.2.0To updateFormat MetaPhlAn2 output to extract abundance at different taxonomic levelsTo updateMetagenomicsformat_metaphlan2_outputbebatuthttps://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/
glimmer_hmmTo updateGlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)To updatehttps://ccb.jhu.edu/software/glimmerhmm/Sequence Analysisglimmer_hmmbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm
graphmap0.5.20.6.3graphmapTo updateMapper for long, error-prone reads.To updatehttps://github.com/isovic/graphmap/Assemblygraphmapbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/graphmap
iprscan5To updateInterproscan queries the interpro database and provides annotations.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisiprscan5bgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/iprscan5
itsx1.1.31.1.3itsxUp-to-dateITSxITSxSequence feature detectionFunctional, regulatory and non-coding RNA, MicrobiologyITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.Up-to-datehttps://microbiology.se/software/itsx/Metagenomicsitsxbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/itsx
lighter1.01.1.2lighterTo updateLighter is a kmer-based error correction method for whole genome sequencing dataTo updateSequence Analysis, Fasta Manipulationlighterbgrueninghttps://github.com/mourisl/Lighter
mafft7.5087.520mafftTo updateMAFFTMAFFTMultiple sequence alignmentSequence analysisMultiple alignment program for amino acid or nucleotide sequencesMAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.To updateRNAmafftrnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/mafft
mcl14.13722.282mclTo updateMarkov Cluster AlgorithmTo updatehttp://micans.org/mcl/Sequence Analysis, Metagenomicsmclbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/mcl
minipolish0.1.30.1.3minipolishUp-to-dateminipolishminipolishLocalised reassemblySequence assemblyPolishing miniasm assembliesA tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.Up-to-datehttps://github.com/rrwick/MinipolishSequence Analysisminipolishbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/minipolish
nextdenovo2.5.02.5.2nextdenovoTo updatenextdenovoNextDenovoDe-novo assembly, Genome assemblySequencing, Sequence assemblyString graph-based de novo assembler for long readsNextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.To updatehttps://github.com/Nextomics/NextDenovoAssemblynextdenovobgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo
nucleosome_prediction3.03.0nucleosome_predictionUp-to-datePrediction of Nucleosomes Positions on the GenomeUp-to-datehttps://genie.weizmann.ac.il/software/nucleo_exe.htmlSequence Analysisnucleosome_predictionbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction
pfamscan1.61.6pfam_scanUp-to-datepfamscanPfamScanProtein sequence analysisSequence analysisSearch a FASTA sequence against a library of Pfam HMM.This tool is used to search a FASTA sequence against a library of Pfam HMM.Up-to-datehttp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/Sequence Analysispfamscanbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/pfamscan
racon1.5.01.5.0raconUp-to-dateConsensus module for raw de novo DNA assembly of long uncorrected reads.Up-to-datehttps://github.com/isovic/raconSequence Analysisraconbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/racon
infernal1.1.41.1.4infernalUp-to-dateinfernalInfernalNucleic acid feature detectionSequence sites, features and motifsInfernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.Up-to-datehttp://infernal.janelia.org/RNAinfernalbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/infernal
rRNA0.1hmmsearch3.0To updateIdentification of ribosomal RNA genes in metagenomic fragments.To updatehttp://weizhong-lab.ucsd.edu/meta_rna/RNArrnarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rRNA
reago1.11.1reagoUp-to-dateReago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.Up-to-datehttps://github.com/chengyuan/reago-1.1Metagenomics, RNAreagornateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago
sortmerna4.3.64.3.6sortmernaUp-to-dateSortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.Up-to-datehttp://bioinfo.lifl.fr/RNA/sortmerna/RNAsortmernarnateamhttps://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna
salmon1.10.11.10.2salmonTo updateSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.To updatehttps://github.com/COMBINE-lab/salmonSequence Analysis, RNA, Transcriptomicsbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/salmon
trim_galore0.6.70.6.10trim-galoreTo updatetrim_galoreTrim GaloreSequence trimmingSequence analysisTrim Galore adaptive quality and adapter trimmerA wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.To updatehttp://www.bioinformatics.babraham.ac.uk/projects/trim_galore/Sequence Analysis, Fastq Manipulationtrim_galorebgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/trim_galore
wtdbg2.52.5wtdbgUp-to-datewtdbg2wtdbg2Genome assembly, De-novo assembly, Mapping assembly, k-mer countingSequence assembly, Computer science, InformaticsWTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.Up-to-datehttps://github.com/ruanjue/wtdbg2Assemblywtdbgbgrueninghttps://github.com/bgruening/galaxytools/tree/master/tools/wtdbg
clinod0.1.01.3clinodTo updateNoD: a Nucleolar localization sequence detector for eukaryotic and viral proteinsTo updatehttp://www.compbio.dundee.ac.uk/www-nod/Sequence Analysisclinodpeterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
effectiveT30.0.201.0.1effectiveT3To updateFind bacterial type III effectors in protein sequencesTo updatehttp://effectors.orgSequence Analysiseffectivet3peterjchttps://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
abricate1.0.11.0.1abricateUp-to-dateABRicateABRicateAntimicrobial resistance predictionGenomics, MicrobiologyMass screening of contigs for antiobiotic resistance genesMass screening of contigs for antimicrobial resistance or virulence genes.Up-to-datehttps://github.com/tseemann/abricateSequence Analysisabricateiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/
abritamr1.0.141.0.14abritamrUp-to-dateA pipeline for running AMRfinderPlus and collating results into functional classesUp-to-datehttps://zenodo.org/record/7370628Sequence Analysisabritamriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr
abyss2.3.62.3.7abyssTo updateabyssABySSGenome assembly, De-novo assemblySequence assemblyAssembly By Short Sequences - a de novo, parallel, paired-end sequence assemblerDe novo genome sequence assembler.To updatehttp://www.bcgsc.ca/platform/bioinfo/software/abyssAssemblyabyssiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss
aldex21.26.01.32.0bioconductor-aldex2To updatealdex2ALDEx2Statistical inferenceGene expression, Statistics and probabilityPerforms analysis Of differential abundance taking sample variation into accountA differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.To updatehttps://github.com/ggloor/ALDEx_biocMetagenomicsaldex2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2
amplican1.14.01.22.1bioconductor-amplicanTo updateamplicanamplicanAlignment, Standardisation and normalisationPCR experiment, Statistics and probabilityAmpliCan is an analysis tool for genome editing.It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.To updatehttps://github.com/valenlab/amplicanSequence Analysisamplicaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican
amrfinderplus3.11.263.11.26ncbi-amrfinderplusUp-to-dateamrfinderplusAMRFinderPlusAntimicrobial resistance predictionMicrobiology, Public health and epidemiology, Infectious disease"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organismsUp-to-datehttps://github.com/ncbi/amrSequence AnalysisAMRFinderPlusiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus
ancombc1.4.02.2.0bioconductor-ancombcTo updateancombcANCOMBCDifferential gene expression profilingMicrobial ecology, MetagenomicsPerforms analysis of compositions of microbiomes with bias correction.Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.To updatehttps://github.com/FrederickHuangLin/ANCOMBCMetagenomicsancombciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc
artic1.2.3articTo updatearticARTICSequence alignmentGenomicsThe 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 buildingA bioinformatics pipeline for working with virus sequencing data sequenced with nanoporeTo updatehttps://github.com/artic-network/fieldbioinformaticsSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/artic
bakta1.8.21.8.2baktaUp-to-dateBaktaBaktaGenome annotationGenomics, Data submission, annotation and curation, Sequence analysis"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."Rapid & standardized annotation of bacterial genomes, MAGs & plasmidsUp-to-datehttps://github.com/oschwengers/baktaSequence Analysisbaktaiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta
bandage2022.092022.09bandage_ngUp-to-datebandageBandageSequence assembly visualisationGenomics, Sequence assemblyBandage - A Bioinformatics Application for Navigating De novo Assembly Graphs EasilyGUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.Up-to-datehttps://github.com/rrwick/BandageVisualizationbandageiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage
bayescan2.12.0.1bayescanTo updatebayescanBayeScanStatistical inferenceGenetics, Evolutionary biology, Statistics and probability, DNA polymorphismDetecting natural selection from population-based genetic dataBAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.To updatehttp://cmpg.unibe.ch/software/BayeScan/index.htmlSequence Analysisbayescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/
binning_refiner1.4.31.4.3binning_refinerUp-to-datebinning_refinerBinning_refinerRead binning, Sequence clusteringMetagenomicsReconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.Improving genome bins through the combination of different binning programsUp-to-datehttps://github.com/songweizhi/Binning_refinerMetagenomicsbinning_refineriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/
biom_format2.1.152.1.7biom-formatTo updateThe biom-format package provides a command line interface and Python API for working with BIOM files.To updatehttps://github.com/biocore/biom-formatMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format
bracken2.82.9brackenTo updatebrackenBrackenStatistical calculationMetagenomics, Microbial ecologyBayesian Reestimation of Abundance with KrakENStatistical method that computes the abundance of species in DNA sequences from a metagenomics sample.To updatehttps://ccb.jhu.edu/software/bracken/Sequence Analysis, Metagenomicsbrackeniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken
busco5.4.65.5.0buscoTo updatebuscoBUSCOSequence assembly validation, Scaffolding, Genome assembly, Transcriptome assemblySequence assembly, Genomics, Transcriptomics, Sequence analysisBUSCO assess genome and annotation completenessProvides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.To updatehttps://gitlab.com/ezlab/busco/-/releasesSequence Analysisbuscoiuc
cat5.2.35.2.3catUp-to-dateContig Annotation Tool (CAT)Up-to-datehttps://github.com/dutilh/CATMetagenomicscontig_annotation_tooliuchttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat
cdhit4.8.14.8.1cd-hitUp-to-datecd-hitcd-hitSequence clusteringSequencingCluster or compare biological sequence datasetsCluster a nucleotide dataset into representative sequences.Up-to-datehttp://weizhongli-lab.org/cd-hit/Sequence Analysis, Fasta Manipulationcd_hitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit
cemitool1.18.11.24.0bioconductor-cemitoolTo updatecemitoolCEMiToolEnrichment analysis, Pathway or network analysisGene expression, Transcriptomics, Microarray experimentGene co-expression network analysis toolIt unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.To updatehttps://www.bioconductor.org/packages/release/bioc/html/CEMiTool.htmlTranscriptomics, RNA, Statisticscemitooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool
checkm1.2.01.2.2checkm-genomeTo updatecheckmCheckMOperationGenomics, Phylogenomics, Phylogenetics, Taxonomy, MetagenomicsAssess the quality of microbial genomes recovered from isolates, single cells, and metagenomesCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.To updatehttps://github.com/Ecogenomics/CheckMMetagenomicscheckmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm
clustalw2.12.1clustalwUp-to-date\n clustalw\nClustalW multiple sequence alignment program for DNA or proteinsUp-to-datehttp://www.clustal.org/clustal2/Phylogenetics, Sequence Analysisclustalwdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw
codeml4.94.10.6pamlTo updateDetects positive selectionTo updatehttp://abacus.gene.ucl.ac.uk/software/paml.htmlPhylogeneticscodemliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml
cojac0.9.10.9.1cojacUp-to-datecojacCOJACGenetic variationco-occurrence of mutations on ampliconsCoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.Up-to-datehttps://github.com/cbg-ethz/cojacMetagenomics, Sequence Analysiscojaciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac
concoct1.1.01.1.0concoctUp-to-dateCONCOCT (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-datehttps://github.com/BinPro/CONCOCTMetagenomicsconcoctiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct
coverm0.6.10.6.1covermUp-to-datecovermCoverMLocal alignmentBioinformaticsCoverM genome and contig wrappersRead coverage calculator for metagenomicsUp-to-datehttps://github.com/wwood/CoverMSequence Analysiscovermiuchttps://github.com/galaxyproject/tools-iuc/tools/coverm
cutadapt4.44.5cutadaptTo updatecutadaptCutadaptSequence trimmingGenomics, Probes and primers, SequencingFlexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.To updatehttps://cutadapt.readthedocs.org/en/stable/Fasta Manipulation, Fastq Manipulation, Sequence Analysiscutadaptlparsonshttps://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
dada21.28.0bioconductor-dada2To updatedada2dada2Variant calling, DNA barcodingSequencing, Genetic variation, Microbial ecology, MetagenomicsDADA2 wrappersThis package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.To updatehttps://benjjneb.github.io/dada2/index.htmlMetagenomicsdada2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2
das_tool1.1.61.1.6das_toolUp-to-datedastooldastoolRead binningMetagenomicsDAS Tool for genome resolved metagenomicsDAS 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.Up-to-datehttps://github.com/cmks/DAS_ToolMetagenomicsdas_tooliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool
diamond2.0.152.1.8diamondTo updateDIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.To updatehttps://github.com/bbuchfink/diamondSequence Analysisdiamondbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond
disco1.2discoTo updatediscoDISCOProtein sequence analysisStructure determinationDISCO is a overlap-layout-consensus (OLC) metagenome assemblerDISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.To updatehttp://disco.omicsbio.org/Metagenomics, Assemblydiscoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/
dram1.3.51.4.6dramTo updateDRAM for distilling microbial metabolism to automate the curation of microbiome functionTo updatehttps://github.com/WrightonLabCSU/DRAMMetagenomicsdramiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/dram
drep3.4.33.4.5drepTo updatedrepdRepGenome comparisonMetagenomics, Genomics, Sequence analysisdRep compares and dereplicates genome setsFast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.To updatehttps://github.com/MrOlm/drepMetagenomicsdrepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/drep
export2graphlan0.200.22export2graphlanTo updateexport2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAnTo updatehttps://bitbucket.org/CibioCM/export2graphlan/overviewMetagenomicsexport2graphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/
fargene0.10.1fargeneUp-to-datefARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )Up-to-datehttps://github.com/fannyhb/fargeneSequence Analysisfargeneiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene
fastp0.23.4fastpTo updateFast all-in-one preprocessing for FASTQ filesTo updatehttps://github.com/OpenGene/fastpSequence Analysisfastpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp
fastqe0.2.6+galaxy20.3.1fastqeTo updateFASTQETo updatehttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqeSequence Analysisfastqeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe
fasttree2.1.102.1.11fasttreeTo updatefasttreeFastTreePhylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Sequence analysisFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVLInfers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.To updatehttp://www.microbesonline.org/fasttree/Phylogeneticsfasttreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree
filtlong0.2.10.2.1filtlongUp-to-date\n filtlong\nFiltlong - Filtering long reads by qualityUp-to-datehttps://github.com/rrwick/FiltlongFastq Manipulation, Sequence Analysisfiltlongiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong
fraggenescan1.31fraggenescanTo updatefraggenescanFragGeneScanGene predictionGenetics, Sequence analysisTool for finding (fragmented) genes in short readApplication for finding (fragmented) genes in short readsTo updatehttps://sourceforge.net/projects/fraggenescan/Sequence Analysisfraggenescaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/
freyja1.4.41.4.7freyjaTo updatefreyjalineage abundances estimationTo updatehttps://github.com/andersen-lab/FreyjaMetagenomics, Sequence Analysisfreyjaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja
funannotate1.8.15To update\n funannotate\nFunannotate is a genome prediction, annotation, and comparison software package.To updatehttps://funannotate.readthedocs.ioGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate
glimmer3.02glimmerTo updategeminiGEMINISequence analysis, Genetic variation analysisSequence analysisGlimmer makes gene predictions.GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.To updatehttps://ccb.jhu.edu/software/glimmer/Sequence Analysisbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer
goenrichment2.0.12.0.1goenrichmentUp-to-dategoenrichmentGOEnrichmentGene-set enrichment analysisTranscriptomicsPerforms GO Enrichment analysis.GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.Up-to-datehttps://github.com/DanFaria/GOEnrichmentGenome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment
goseq1.50.01.52.0bioconductor-goseqTo updategoseqGOseqGene functional annotationRNA-seqgoseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq dataDetect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.To updatehttps://bioconductor.org/packages/release/bioc/html/goseq.htmlStatistics, RNA, Micro-array Analysisgoseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq
graphlan1.1.3graphlanTo updateGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic treesTo updatehttps://bitbucket.org/nsegata/graphlan/overviewMetagenomics, Graphics, Phylogeneticsgraphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/
gtdbtk2.2.22.3.2gtdbtkTo updateGTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.To updatehttps://github.com/Ecogenomics/GTDBTkMetagenomicsgtdbtkiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk
gubbins3.2.13.3.1gubbinsTo updategubbinsGubbinsGenotyping, Phylogenetic inference, Ancestral reconstructionPhylogeny, Genotype and phenotype, Whole genome sequencingGubbins - bacterial recombination detectionGubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.To updateSequence Analysisgubbinsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins
hamronization1.0.31.1.4hamronizationTo updateConvert AMR gene detection tool output to hAMRonization specification format.To updatehttps://github.com/pha4ge/hAMRonizationSequence Analysishamronizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization
hansel2.6.12.6.1bio_hanselUp-to-dateHeidelberg and Enteritidis SNP ElucidationUp-to-datehttps://github.com/phac-nml/bio_hanselSequence Analysisbio_hanseliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel
hifiasm_meta0.3.1hamtv0.3.1hifiasm_metaTo updateA hifiasm fork for metagenome assembly using Hifi reads.To updatehttps://github.com/xfengnefx/hifiasm-metaMetagenomicshifiasm_metagalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta
hmmer33.3.23.3.2hmmerUp-to-datehmmer3HMMER3Formatting, 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 searchSequence analysis, Sequence sites, features and motifs, Gene and protein familiesHMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.Up-to-datehttp://hmmer.org/Sequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3
humann3.83.8humannUp-to-datehumannhumannSpecies frequency estimation, Taxonomic classification, Phylogenetic analysisMetagenomics, PhylogenomicsHUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolutionHUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”Up-to-datehttp://huttenhower.sph.harvard.edu/humannMetagenomicshumanniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/humann
hyphy2.5.472.5.50hyphyTo updateHyPhyHyPhyStatistical calculationPhylogeny, Small molecules, Molecular interactions, pathways and networksHypothesis Testing using PhylogeniesSoftware package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.To updatehttp://www.hyphy.orgPhylogeneticsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/
hypo1.0.31.0.3hypoUp-to-dateHyPoHyPoOptimisation and refinement, Genome assemblySequence assembly, GenomicsSuper Fast & Accurate Polisher for Long Read Genome AssembliesHyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.Up-to-datehttps://github.com/kensung-lab/hypoAssemblyhypoiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo
icescreen1.2.01.2.0icescreenUp-to-dateICEscreenICEscreenDatabase search, Protein feature detectionMobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variationICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Firmicutes genomes.A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.Up-to-datehttps://icescreen.migale.inrae.fr/Genome annotationicescreeniuchttps://forgemia.inra.fr/ices_imes_analysis/icescreen
idba_ud1.1.3idbaTo updateidbaIDBASequence assemblySequence assemblyWrappers for the idba assembler variants.A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.To updatehttps://i.cs.hku.hk/~alse/hkubrg/projects/index.htmlAssemblyidbaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud
instrain1.5.31.8.0instrainTo updateInStrain is a tool for analysis of co-occurring genome populations from metagenomesTo updatehttps://instrain.readthedocs.io/en/latest/#Metagenomicsinstrainiuchttps://github.com/MrOlm/inStrain
interproscan5.59-91.05.59_91.0interproscanTo updateinterproscan_ebiInterProScan (EBI)Sequence motif recognition, Protein feature detectionGene and protein families, Sequence analysisInterproscan queries the interpro database and provides annotations.Scan sequences against the InterPro protein signature databases.To updatehttp://www.ebi.ac.uk/Tools/pfa/iprscan5/Sequence Analysisinterproscanbgrueninghttps://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan
iqtree2.1.22.2.5iqtreeTo updateEfficient phylogenomic software by maximum likelihoodTo updatehttp://www.iqtree.org/Phylogeneticsiqtreeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/
ivar1.4.21.4.2ivarUp-to-dateiVar is a computational package that contains functions broadly useful for viral amplicon-based sequencingUp-to-datehttps://github.com/andersen-lab/ivarSequence Analysisivariuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/
jbrowse1.16.111.16.11jbrowseUp-to-datejbrowseJBrowseGenome visualisationGenomicsJBrowse Genome Browser integrated as a Galaxy ToolSlick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.Up-to-datehttps://jbrowse.orgSequence Analysisjbrowseiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
jellyfish2.3.0kmer-jellyfishTo updateJellyfishJellyfishk-mer countingSequence analysis, GenomicsJellyfish is a tool for fast, memory-efficient counting of k-mers in DNAA command-line algorithm for counting k-mers in DNA sequence.To updatehttps://github.com/gmarcais/JellyfishAssemblyjellyfishiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish
kc-align1.0.21.0.2kcalignUp-to-datekc-alignkc-alignMultiple sequence alignmentMappingKc-Align custom toolA fast and accurate tool for performing codon-aware multiple sequence alignmentsUp-to-datehttps://github.com/davebx/kc-alignSequence Analysiskc_aligniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align
khmer3.0.0a33.0.0a3khmerUp-to-datekhmerkhmerStandardisation and normalisation, De-novo assemblySequence assemblyIn-memory nucleotide sequence k-mer counting, filtering, graph traversal and morekhmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.Up-to-datehttps://khmer.readthedocs.org/Assembly, Next Gen Mapperskhmeriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer
kleborate2.3.22.3.2kleborateUp-to-datekleborateKleborateMultilocus sequence typing, Genome assembly, Virulence predictionPublic health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencingScreen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).Up-to-datehttps://github.com/katholt/Kleborate/wikiMetagenomicskleborateiuchttps://github.com/katholt/Kleborate
kofamscan1.3.01.3.0kofamscanUp-to-dateGene function annotation tool based on KEGG Orthology and hidden Markov modelUp-to-datehttps://github.com/takaram/kofam_scanSequence Analysiskofamscaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan
kraken_biom1.2.01.2.0kraken-biomUp-to-dateCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)Up-to-datehttps://github.com/smdabdoub/kraken-biomMetagenomicskraken_biomiuchttps://github.com/smdabdoub/kraken-biom
kraken_taxonomy_report0.0.31.70biopythonTo updateKraken taxonomy reportTo updatehttps://github.com/blankenberg/Kraken-Taxonomy-ReportMetagenomicskraken_taxonomy_reportiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report
krakentools1.21.2krakentoolsUp-to-datekrakentoolsKrakenToolsVisualisation, AggregationTaxonomy, MetagenomicsKrakenTools is a suite of scripts to be used alongside the KrakenKrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output filesUp-to-datehttps://github.com/jenniferlu717/KrakenToolsMetagenomicskrakentoolsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools
krocus1.0.11.0.3krocusTo updatePredict MLST directly from uncorrected long readsTo updatehttps://github.com/quadram-institute-bioscience/krocusSequence Analysiskrocusiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus
legsta0.5.10.5.1legstaUp-to-datePerforms in silico Legionella pneumophila sequence based typing.Up-to-datehttps://github.com/tseemann/legstaSequence Analysislegstaiuchttps://github.com/tseemann/legsta
lineagespot1.4.0r-baseTo updatelineagespotlineagespotVariant callingMetagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variationIdentification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).To updatehttps://www.bioconductor.org/packages/release/bioc/html/lineagespot.htmlMetagenomics, Sequence Analysislineagespotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot
lorikeet2020lorikeetUp-to-dateTools for M. tuberculosis DNA fingerprinting (spoligotyping)Up-to-datehttps://github.com/AbeelLab/lorikeetSequence Analysislorikeet_spoligotypeiuchttps://github.com/AbeelLab/lorikeet
m6anet2.1.02.1.0m6anetUp-to-datem6Anetm6AnetQuantification, Imputation, Gene expression profilingRNA-Seq, Transcriptomics, RNA, Machine learningm6anet to detect m6A RNA modifications from nanopore dataDetection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.Up-to-datehttps://m6anet.readthedocs.io/en/latestSequence Analysism6anetiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet
maaslin20.99.120.99.12maaslin2Up-to-dateMaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.Up-to-datehttp://huttenhower.sph.harvard.edu/maaslinMetagenomicsmaaslin2iuchttps://github.com/biobakery/Maaslin2
maker2.31.113.01.03makerTo updatemakerMAKERGenome annotationGenomics, DNA, Sequence analysisMAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.To updatehttp://www.yandell-lab.org/software/maker.htmlSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maker
mapseq2.1.1perlTo updatefast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.To updatehttps://github.com/jfmrod/MAPseqMetagenomicsmapseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq
mash2.32.3mashUp-to-datemashMashSequence distance matrix generationGenomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutationFast genome and metagenome distance estimation using MinHashFast genome and metagenome distance estimation using MinHash.Up-to-datehttps://github.com/marbl/MashMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mash
maxbin22.2.7maxbin2To updatemaxbinMaxBinSequence assemblyMetagenomics, Sequence assembly, Microbiologyclusters metagenomic contigs into binsSoftware for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.To updatehttps://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.htmlMetagenomicsmaxbin2mbernthttps://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/
medaka1.7.21.11.1medakaTo updatemedakaMedakaBase-calling, Variant calling, Sequence assemblySequence assembly, Machine learningSequence correction provided by ONT Researchmedaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.To updatehttps://github.com/nanoporetech/medakaSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka
megahit1.2.91.2.9megahitUp-to-datemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.Up-to-datehttps://github.com/voutcn/megahitSequence Analysis, Assembly, Metagenomicsmegahitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit
megahit_contig2fastg1.1.31.2.9megahitTo updatemegahitMEGAHITGenome assemblyMetagenomics, Sequencing, Ecology, Sequence assemblyA subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.To updatehttps://github.com/voutcn/megahit/blob/master/tools/toolkit.cppSequence Analysis, Assembly, Metagenomicsmegahit_contig2fastgiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg
megan6.21.76.24.20meganTo updatemeganMEGANSequence analysis, Taxonomic classificationSequence analysisMEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.To updatehttps://github.com/husonlab/megan-ceSequence Analysismeganiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/megan
meningotype0.8.50.8.5meningotypeUp-to-dateAssign sequence type to N. meningitidis genome assembliesUp-to-datehttps://github.com/MDU-PHL/meningotypeSequence Analysismeningotypeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype
merqury1.31.3merquryUp-to-datemerquryMerquryGenome assembly, k-mer counting, Scaffolding, Phasing, De-novo assemblySequence assembly, Whole genome sequencing, Plant biologyMerqury is a tool for evaluating genomes assemblies based of k-mer operations.Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.Up-to-datehttps://github.com/marbl/merquryAssemblymerquryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury
meryl1.31.3merquryUp-to-dateMeryl a k-mer counter.Up-to-datehttps://github.com/marbl/merylAssemblymeryliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
metabat22.152.15metabat2Up-to-dateMetaBAT2 (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-datehttps://bitbucket.org/berkeleylab/metabat/src/master/Metagenomicsmetabat2iuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/
metaeuk5.34c21f26.a5d39d9metaeukTo updateMetaEukMetaEukHomology-based gene predictionMetagenomics, Gene and protein familiesMetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomicsTo updatehttps://github.com/soedinglab/metaeukSequence Analysis, Genome annotationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk
metagenomeseq1.16.0-0.0.11.42.0bioconductor-metagenomeseqTo updatemetagenomeseqmetagenomeSeqSequence visualisation, Statistical calculationMetagenomics, SequencingmetagenomeSeq NormalizationDesigned to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.To updateMetagenomicsmetagenomeseq_normalizationiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq
metaphlan4.0.64.0.6metaphlanUp-to-datemetaphlanMetaPhlAnNucleic acid sequence analysis, Phylogenetic tree analysisMetagenomics, PhylogenomicsMetaPhlAn for Metagenomic Phylogenetic AnalysisComputational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.Up-to-datehttps://github.com/biobakery/MetaPhlAnMetagenomicsmetaphlaniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/
minia3.2.63.2.6miniaUp-to-dateminiaMiniaGenome assemblySequence assemblyShort-read assembler based on a de Bruijn graphShort-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.Up-to-datehttps://gatb.inria.fr/software/minia/Assemblyminiaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
miniasm0.3_r1790.3miniasmTo updateMiniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)To updatehttps://github.com/lh3/miniasmAssemblyminiasmiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm
miniprot0.120.12miniprotUp-to-dateAlign a protein sequence against a genome with affine gap penalty, splicing and frameshift.Up-to-datehttps://github.com/lh3/miniprotSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot
mitos1.1.12.1.3mitosTo updatemitosMITOSGenome annotationZoology, Whole genome sequencingde-novo annotation of metazoan mitochondrial genomesDe novo metazoan mitochondrial genome annotation.To updatehttp://mitos.bioinf.uni-leipzig.de/Sequence Analysismitosiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos
mlst2.22.02.23.0mlstTo updatemlstMLSTTaxonomic classificationImmunoproteins, genes and antigensScan contig files against PubMLST typing schemesMulti Locus Sequence Typing from an assembled genome or from a set of reads.To updatehttps://github.com/tseemann/mlstSequence Analysismlstiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst
mothur1.01.48.0mothurTo updateMothur wrappersTo updatehttps://www.mothur.orgMetagenomicsmothuriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur
multigsea1.8.01.10.0bioconductor-multigseaTo updatemultiGSEAmultiGSEAGene-set enrichment analysis, Aggregation, Pathway analysisMetabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small moleculesGSEA-based pathway enrichment analysis for multi-omics dataA GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.To updatehttps://bioconductor.org/packages/devel/bioc/html/multiGSEA.htmlTranscriptomics, Proteomics, Statisticsmultigseaiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea
multiqc1.111.17multiqcTo updatemultiqcMultiQCValidationSequencing, BioinformaticsMultiQC aggregates results from bioinformatics analyses across many samples into a single reportMultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.To updatehttp://multiqc.info/Fastq Manipulation, Statistics, Visualizationmultiqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc
mykrobe0.10.00.13.0mykrobeTo updateMykrobeMykrobeAntimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimmingWhole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, MetagenomicsAntibiotic resistance predictionsAntibiotic 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 installedTo updatehttps://github.com/Mykrobe-tools/mykrobeSequence Analysismykrobeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe
nanocompore1.0.0rc3.post21.0.4nanocomporeTo updateNanocomporeNanocomporePost-translation modification site prediction, PolyA signal detection, Genotyping, k-mer countingFunctional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sitesNanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitroTo updatehttps://nanocompore.rna.rocks/Sequence Analysisnanocomporeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore
nanoplot1.41.01.42.0nanoplotTo updatePlotting tool for long read sequencing data and alignmentsTo updatehttps://github.com/wdecoster/NanoPlotVisualizationnanoplotiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/
nanopolishcomp0.6.110.6.12nanopolishcompTo updateNanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.To updatehttps://a-slide.github.io/NanopolishCompSequence Analysisnanopolishcompiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp
newick_utils1.6+galaxy11.6newick_utilsTo updatenewick_utilitiesNewick UtilitiesPhylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstructionPhylogeny, Genomics, Computer sciencePerform operations on Newick treesThe Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.To updatehttp://cegg.unige.ch/newick_utilsVisualization, Metagenomicsnewick_utilsiuchttps://github.com/tjunier/newick_utils
nextclade2.7.02.14.0nextalignTo updateIdentify differences between your sequences and a reference sequence used by NextstrainTo updatehttps://github.com/nextstrain/nextcladeSequence Analysisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade
nonpareil3.1.13.4.1nonpareilTo updateEstimate average coverage in metagenomic datasetsTo updatehttp://nonpareil.readthedocs.ioMetagenomicsnonpareiliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil
nugen_nudup2.3.32.3.3nudupUp-to-dateMarks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.Up-to-datehttp://nugentechnologies.github.io/nudup/SAM, Metagenomics, Sequence Analysis, Transcriptomicsnugen_nudupiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup
orfipy0.0.40.0.4orfipyUp-to-dateorfipyorfipyCoding region prediction, Database search, Transcriptome assembly, De-novo assemblyComputer science, RNA-Seq, Transcriptomics, Small moleculesGalaxy wrapper for ORFIPYA fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.Up-to-datehttps://github.com/urmi-21/orfipySequence Analysisorfipyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy
orthofinder2.5.42.5.5orthofinderTo updateOrthoFinderOrthoFinderGenome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignmentPhylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysisAccurate inference of orthologous gene groups made easyOrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.To updatehttps://github.com/davidemms/OrthoFinderPhylogenetics, Sequence Analysisorthofinderiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder
pharokka1.3.2\n pharokka\nTo update\n pharokka\nrapid standardised annotation tool for bacteriophage genomes and metagenomesTo updatehttps://github.com/gbouras13/pharokkaGenome annotationpharokkaiuchttps://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
phyloseq1.38.01.44.0bioconductor-phyloseqTo updateHandling and analysis of high-throughput microbiome census dataTo updatehttps://www.bioconductor.org/packages/release/bioc/html/phyloseq.htmlMetagenomicsphyloseqiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq
phyml3.3.202204083.3.20220408phymlUp-to-datephymlPhyMLPhylogenetic tree generation (maximum likelihood and Bayesian methods)Phylogenetics, Bioinformatics, PhylogeneticsPhyML is a phylogeny software based on the maximum-likelihood principle.Phylogenetic estimation software using Maximum LikelihoodUp-to-datehttp://www.atgc-montpellier.fr/phyml/Phylogeneticsphymliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml
picrust1.1.11.1.4picrustTo updatePICRUSt wrappersTo updatehttps://picrust.github.io/picrust/Metagenomicspicrustiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust
picrust22.5.12.5.2picrust2To updatepicrust2PICRUSt2Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysisMetagenomics, Microbiology, Phylogenetics, Metagenomic sequencingPICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved StatesPICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.To updatehttps://github.com/picrust/picrust2/wikiMetagenomicspicrust2iuchttps://github.com/picrust/picrust2
plasflow1.1.01.1.0plasflowUp-to-datePlasFlow - Prediction of plasmid sequences in metagenomic contigs.Up-to-datehttps://github.com/smaegol/PlasFlowSequence Analysisplasflowiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow
plasmidfinder2.1.62.1.6plasmidfinderUp-to-datePlasmidFinderPlasmidFinderGenome assembly, Scaffolding, Multilocus sequence typingWhole genome sequencing, Sequence assembly, Mapping, Probes and primers"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).Up-to-datehttps://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/Sequence Analysisplasmidfinderiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder
prokka1.14.61.14.6prokkaUp-to-dateprokkaProkkaGene prediction, Coding region prediction, Genome annotationGenomics, Model organisms, VirologyRapid annotation of prokaryotic genomesSoftware tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.Up-to-datehttp://github.com/tseemann/prokkaSequence Analysisprokkacrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/
proteinortho6.2.36.3.0proteinorthoTo updateproteinorthoProteinorthoHomology-based gene predictionPhylogenyProteinortho is a tool to detect orthologous proteins/genes within different species.Proteinortho is a tool to detect orthologous genes within different speciesTo updatehttps://gitlab.com/paulklemm_PHD/proteinorthoProteomicsproteinorthoiuchttps://gitlab.com/paulklemm_PHD/proteinortho
pycoqc2.5.22.5.2pycoqcUp-to-dateQC metrics for ONT BasecallingUp-to-datehttps://github.com/tleonardi/pycoQCNanoporepycoqciuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc
pygenometracks3.83.8pygenometracksUp-to-datepyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.Up-to-datehttps://github.com/deeptools/pyGenomeTracksVisualizationpygenometracksiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks
qiime_add_on1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qiime_core1.9.1qiimeTo updateQIIME to perform microbial community analysisTo updatehttp://www.qiime.orgMetagenomicsqiimeiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/
qualimap2.2.2d2.2.2dqualimapUp-to-datequalimapQualiMapSequencing quality controlData quality managementPlatform-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.Up-to-datehttp://qualimap.bioinfo.cipf.es/Sequence Analysis, Transcriptomics, SAMqualimapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap
quast5.2.05.2.0quastUp-to-datequastQUASTVisualisation, Sequence assembly validationSequence assemblyQuast (Quality ASsessment Tool) evaluates genome assemblies.QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.Up-to-datehttp://quast.bioinf.spbau.ru/Assemblyquastiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quast
quickmerge0.30.3quickmergeUp-to-datequickmergequickmergeGenome assembly, Scaffolding, De-novo assembly, GenotypingStructural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotypeMerge long-read and hybrid assemblies to increase contiguityQuickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.Up-to-datehttps://github.com/mahulchak/quickmergeAssemblyquickmergegalaxy-australiahttps://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge
raxml8.2.128.2.13raxmlTo updateraxmlRAxMLSequence analysis, Phylogenetic tree analysisPhylogenetics, Sequence analysisRAxML - A Maximum Likelihood based phylogenetic inferenceA tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.To updatehttp://www.exelixis-lab.org/web/software/raxml/Phylogeneticsraxmliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml
read_it_and_keep0.2.20.3.0read-it-and-keepTo updateRapid decontamination of SARS-CoV-2 sequencing readsTo updatehttps://github.com/GenomePathogenAnalysisService/read-it-and-keepSequence Analysisread_it_and_keepiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep
recentrifuge1.12.11.12.1recentrifugeUp-to-dateRecentrifugeRecentrifugeTaxonomic classification, Expression analysis, Cross-assemblyMetagenomics, Microbial ecology, Metagenomic sequencing"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."Robust comparative analysis and contamination removal for metagenomics.Up-to-datehttps://github.com/khyox/recentrifugeMetagenomicsrecentrifugeiuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge
roary3.13.03.13.0roaryUp-to-dateroaryRoaryGenome assemblyDNA, Genomics, MappingRoary the pangenome pipelineA high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.Up-to-datehttps://sanger-pathogens.github.io/Roary/Sequence Analysisroaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/roary
rseqc5.0.15.0.3rseqcTo updaterseqcRSeQCData handlingSequencingan RNA-seq quality control packageProvides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.To updatehttps://code.google.com/p/rseqc/Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualizationrseqcnileshhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc
sarscov2formatter1.01.0sarscov2formatterUp-to-datesarscov2formatter custom scriptUp-to-datehttps://github.com/nickeener/sarscov2formatterSequence Analysissarscov2formatteriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter
sarscov2summary0.10.5sarscov2summaryTo updatesarscov2summary custom scriptTo updatehttps://github.com/nickeener/sarscov2summarySequence Analysissarscov2summaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary
scoary1.6.161.6.16scoaryUp-to-dateScoary calculates the assocations between all genes in the accessory genome and the traits.Up-to-datehttps://github.com/AdmiralenOla/ScoaryMetagenomicsscoaryiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary
semibin1.5.12.0.2semibinTo updatesemibinSemiBinSequence assembly, Read binning, VisualisationMetagenomics, Machine learning, Microbial ecology, Sequence assemblySemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural NetworksCommand tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.To updatehttps://semibin.readthedocs.io/en/latest/Metagenomicssemibiniuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin
seqkit2.3.12.5.1seqkitTo updateseqkitseqkitDNA transcription, Sequence trimming, DNA translation, Sequence conversionDatabase management, Sequence analysisA cross-platform and ultrafast toolkit for FASTA/Q file manipulationFASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.To updatehttps://bioinf.shenwei.me/seqkit/Sequence Analysisseqkitiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit
shovill1.1.01.1.0shovillUp-to-dateshovillshovillGenome assemblyGenomics, Microbiology, Sequence assemblyFaster de novo assembly pipeline based around SpadesShovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.Up-to-datehttps://github.com/tseemann/shovillAssemblyshovilliuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill
smallgenomeutilities0.4.00.4.0smallgenomeutilitiesUp-to-datev-pipeV-pipeRead pre-processing, Sequence alignment, Genetic variation analysisGenomics, Population genetics, Workflows, Virology, SequencingSet of utilities for manipulating small viral genome data.Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.Up-to-datehttps://github.com/cbg-ethz/smallgenomeutilitiesSequence Analysissmallgenomeutilitiesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities
snap2013_11_292013_11_29snapUp-to-datesnapSNAPGene predictionDNA, DNA polymorphism, GeneticsSNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.Up-to-datehttps://github.com/KorfLab/SNAPSequence Analysissnapiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snap
snippy4.6.0snippyTo updatesnippysnippyPhylogenetic tree visualisation, Phylogenetic tree generation, Variant callingGenomics, Model organisms, DNA polymorphism, PhylogeneticsContains the snippy tool for characterising microbial snpsRapid haploid variant calling and core SNP phylogeny generation.To updatehttps://github.com/tseemann/snippySequence Analysissnippyiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy
sonneityping2021020120210201sonneitypingUp-to-dateScripts for parsing Mykrobe predict results for Shigella sonnei.Up-to-datehttps://github.com/katholt/sonneitypingSequence Analysissonneitypingiuchttps://github.com/katholt/sonneityping
spades3.15.53.15.5spadesUp-to-dateSPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.Up-to-datehttps://github.com/ablab/spadesAssembly, RNA, Metagenomicsspadesiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/spades
spotyping2.12.1spotypingUp-to-datespotypingSpoTypingVariant pattern analysisMicrobiology, Sequencing, Sequence composition, complexity and repeats, Genetic variationSpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence readsFast and accurate in silico Mycobacterium spoligotyping from sequence reads.Up-to-datehttps://github.com/xiaeryu/SpoTyping-v2.0Sequence Analysisspotypingiuchttps://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine
srst20.2.01.18samtoolsTo updateSRST2 Short Read Sequence Typing for Bacterial PathogensTo updatehttp://katholt.github.io/srst2/Metagenomicssrst2iuchttps://github.com/katholt/srst2
structure2.3.42.3.4structureUp-to-datestructureStructureGenetic variation analysisPopulation geneticsfor using multi-locus genotype data to investigate population structure.The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.Up-to-datePhylogenetics, Variant Analysisstructureiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/structure
taxonomy_krona_chart2.7.1+galaxy02.8.1kronaTo updatekronaKronaVisualisationMetagenomicsKrona pie chart from taxonomic profileKrona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).To updatehttp://sourceforge.net/projects/krona/Assemblytaxonomy_krona_chartcrs4https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart
tb-profiler4.4.15.0.1tb-profilerTo updateProcesses M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.To updatehttps://github.com/jodyphelan/TBProfilerSequence Analysistbprofileriuchttps://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler
transtermhp2.09transtermhpTo updateFinds rho-independent transcription terminators in bacterial genomesTo updateSequence Analysistranstermhpiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp
unicycler0.5.00.5.0unicyclerUp-to-dateunicyclerUnicyclerGenome assembly, AggregationMicrobiology, Genomics, Sequencing, Sequence assemblyUnicycler is a hybrid assembly pipeline for bacterial genomes.A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.Up-to-datehttps://github.com/rrwick/UnicyclerAssemblyunicycleriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler
usher0.2.10.6.2usherTo updateUShER toolkit wrappersTo updatehttps://github.com/yatisht/usherPhylogeneticsusheriuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/usher
valet1.0valetTo updateA pipeline for detecting mis-assemblies in metagenomic assemblies.To updatehttps://github.com/marbl/VALETMetagenomicsvaletiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/valet
vapor1.0.21.0.2vaporUp-to-datevaporVAPORData retrieval, De-novo assembly, Read mappingWhole genome sequencing, Mapping, Sequence assemblyClassify Influenza samples from raw short read sequence dataVAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.Up-to-datehttps://github.com/connor-lab/vaporSequence Analysisvaporiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor
vegan2.4-32.3_4r-veganTo updateTo updatehttps://cran.r-project.org/package=veganMetagenomicsiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/
velvet1.2.10velvetTo updatevelvetVelvetFormatting, De-novo assemblySequence assemblyde novo genomic assembler specially designed for short read sequencing technologiesA de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.To updatehttps://www.ebi.ac.uk/~zerbino/velvet/Assemblyvelvetdevteamhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet
velvet_optimiser2.2.6+galaxy21.2.10velvetTo updatevelvetoptimiserVelvetOptimiserOptimisation and refinement, Sequence assemblyGenomics, Sequence assemblyAutomatically optimize Velvet assembliesThis tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.To updateAssemblyvelvetoptimisersimon-gladmanhttps://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser
vsearch2.8.32.24.0vsearchTo updatevsearchVSEARCHDNA mapping, Chimera detectionMetagenomics, Sequence analysisVSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.To updatehttps://github.com/torognes/vsearchSequence Analysisvsearchiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch
bamtools2.5.22.5.2bamtoolsUp-to-dateOperate on and transform BAM datasets in various ways using bamtoolsUp-to-datehttps://github.com/pezmaster31/bamtoolsSequence Analysis, SAMbamtoolsdevteamhttps://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools
biotradis1.4.51.4.5biotradisUp-to-dateBio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.Up-to-datehttps://www.sanger.ac.uk/science/tools/bio-tradisGenome annotationbiotradisiuchttps://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis
kraken1.1.1krakenTo updateKraken 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 updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskrakendevteamhttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/
kraken22.1.12.1.3kraken2To updateKraken2 for taxonomic designation.To updatehttp://ccb.jhu.edu/software/kraken/Metagenomicskraken2iuchttps://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/
eggnog_mapper2.1.82.1.12eggnog-mapperTo updateeggnog-mapper-v2eggNOG-mapper v2Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrievalMetagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysiseggnog-mapper fast functional annotation of novel sequencesEggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.To updateProteomicseggnog_mappergalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper
metagene_annotator1.0.01.0metagene_annotatorTo updateMetaGeneAnnotator gene-finding program for prokaryote and phageTo updateSequence Analysismetagene_annotatorgalaxyphttps://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
PAMPA0.0.2To updateTools to compute and analyse biodiversity metricsTo updateEcologypampaecologyhttps://github.com/ColineRoyaux/PAMPA-Galaxy
obisindicators0.0.2r-baseTo updateCompute biodiveristy indicators for marine data from obisTo updateEcologyecologyhttps://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators
+ +
\ No newline at end of file diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv new file mode 100644 index 00000000..1195fd8b --- /dev/null +++ b/results/microgalaxy/tools.tsv @@ -0,0 +1,731 @@ +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 Reviewed To keep +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 True False +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 True False +helixer helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 True False +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 True False +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest 2.0 True False +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ 0.3.1 True False +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 True True +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 True False +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 True True +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b True False +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 True False +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 True False +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 True True +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 True False +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 True False +t_coffee t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b True False +abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas 1.1 mummer 3.23 True True +assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 True True +bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools 1.1.0 perl True False +bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Up-to-date https://github.com/tommyau/bamclipper Sequence Analysis bamclipper nml https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 True False +biohansel biohansel Heidelberg and Enteritidis SNP Elucidation To update https://github.com/phac-nml/biohansel Sequence Analysis biohansel nml https://github.com/phac-nml/biohansel 2.4.0 bio_hansel 2.6.1 True True +bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download To update Sequence Analysis bundle_collections nml 1.3.0 perl-getopt-long 2.54 True False +collapse_collection collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection To update Sequence Analysis collapse_collections nml 5.1.0 gawk True False +combineJSON combine_json JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. To update Sequence Analysis combine_json nml 0.1 True False +combine_assembly_stats combine_stats Combine multiple Assemblystats datasets into a single tabular report To update https://github.com/phac-nml/galaxy_tools Assembly combine_assemblystats nml https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.54 True True +combine_tabular_collection combine Combine Tabular Collection into a single file To update Sequence Analysis combine_tabular_collection nml 0.1 True False +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 True True +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 True True +fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fasta2bed nml https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 True False +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 True False +fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report To update https://github.com/phac-nml/galaxy_tools Sequence Analysis fastqc_stats nml https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 True False +feht feht Automatically identify makers predictive of groups. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis feht nml https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 True False +filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds To update https://github.com/phac-nml/galaxy_tools/ Assembly filter_spades_repeats nml https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 True True +getmlst getmlst Download MLST datasets by species from pubmlst.org To update Sequence Analysis getmlst nml 0.1.4.1 srst2 0.2.0 True True +hivtrace hivtrace An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. To update Sequence Analysis hivtrace nml https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace 1.0.1 hivtrace 1.5.0 True True +kaptive kaptive Kaptive reports information about capsular (K) loci found in genome assemblies. To update Sequence Analysis kaptive nml 0.3.0 kaptive 2.0.6 True False +kat_filter kat_@EXECUTABLE@ Filtering kmers or reads from a database of kmers hashes To update Sequence Analysis kat_filter nml 2.3 kat 2.4.2 True True +mauve_contig_mover mauve_contig_mover Order a draft genome relative to a related reference genome To update https://github.com/phac-nml/mauve_contig_mover Sequence Analysis mauve_contig_mover nml https://github.com/phac-nml/mauve_contig_mover 1.0.10 mauve 2.4.0.r4736 True False +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 True True +mrbayes mrbayes A program for the Bayesian estimation of phylogeny. To update Sequence Analysis mrbayes nml 1.0.2 mrbayes 3.2.7 True True +mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. To update https://github.com/phac-nml/mykrobe-parser Sequence Analysis mykrobe_parser nml https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base True True +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 True False +patrist patrist Extract Patristic Distance From a Tree To update https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 Phylogenetics patrist nml https://github.com/phac-nml/patrist 0.1.2 python True False +plasmid_profiler_suite Plasmid Profiler suite defining all dependencies for Plasmid Profiler To update Sequence Analysis suite_plasmid_profiler nml True False +plasmidspades plasmidspades Genome assembler for assemblying plasmid To update Assembly plasmidspades nml 1.1 spades 3.15.5 True True +promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them To update https://github.com/phac-nml/promer Assembly promer nml https://github.com/phac-nml/promer 1.2 python True True +pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. To update https://github.com/phac-nml/galaxy_tools Sequence Analysis pseudogenome nml 1.0.0 perl-bioperl 1.7.8 True False +quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies Up-to-date https://github.com/phac-nml/quasitools Sequence Analysis quasitools nml https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 True False +refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. Up-to-date https://github.com/phac-nml/refseq_masher Sequence Analysis refseq_masher nml https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 True False +seqtk_nml seqtk_nml_sample Tool to downsample fastq reads To update https://github.com/lh3/seqtk Sequence Analysis seqtk_nml nml https://github.com/phac-nml/snvphyl-galaxy 1.0.1 seqtk 1.4 True False +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 True True +smalt smalt SMALT aligns DNA sequencing reads with a reference genome. Up-to-date http://www.sanger.ac.uk/science/tools/smalt-0 Sequence Analysis smalt nml https://sourceforge.net/projects/smalt/ 0.7.6 smalt 0.7.6 True True +spatyper spatyper Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. Up-to-date https://github.com/HCGB-IGTP/spaTyper Sequence Analysis spatyper nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper 0.3.3 spatyper 0.3.3 True False +spolpred spolpred A program for predicting the spoligotype from raw sequence reads To update Sequence Analysis spolpred nml 1.0.1 spolpred True False +srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens To update Sequence Analysis srst2 nml 0.3.7 srst2 0.2.0 True True +staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. Up-to-date https://github.com/phac-nml/staramr Sequence Analysis staramr nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 0.10.0 staramr 0.10.0 True True +stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) To update Sequence Analysis stringmlst nml 1.1.0 stringMLST 0.6.3 True True +wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade 0.2.5+galaxy1 wade 0.2.6 True False +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 True False +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 True False +blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 1.0.0 True False +blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping 1.0.0 True False +cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads To update Metagenomics, Sequence Analysis cd_hit_dup devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup 0.0.1 cd-hit-auxtools 4.8.1 True True +compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. To update Sequence Analysis, Statistics compute_motif_frequencies_for_all_motifs devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs 1.0.0 True False +compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. To update Sequence Analysis, Statistics compute_motifs_frequency devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency 1.0.0 True False +count_gff_features count_gff_features Count GFF Features To update Sequence Analysis count_gff_features devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features 0.2 galaxy-ops 1.1.0 True False +ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes To update Sequence Analysis ctd_batch devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch 1.0.0 True False +cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library To update https://bioconductor.org/packages/release/bioc/html/cummeRbund.html RNA, Visualization cummerbund devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund 2.16.0 fonts-conda-ecosystem True False +delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file To update Sequence Analysis delete_overlapping_indels devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels 1.0.0 True False +divide_pg_snp dividePgSnp Separate pgSnp alleles into columns To update Sequence Analysis divide_pg_snp devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp 1.0.0 True False +express express Quantify the abundances of a set of target sequences from sampled subsequences To update RNA express devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express 1.1.1 eXpress 1.5.1 True False +featurecounter featureCoverage1 Feature coverage To update Sequence Analysis, Variant Analysis featurecounter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter 2.0.0 bx-python 0.10.0 True False +filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts To update RNA filter_transcripts_via_tracking devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking 0.1 True False +generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA To update Sequence Analysis generate_pc_lda_matrix devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix 1.0.0 True False +getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments To update Sequence Analysis, Variant Analysis getindelrates_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way 1.0.0 bx-python 0.10.0 True False +getindels_2way getIndels_2way Fetch Indels from pairwise alignments To update Sequence Analysis, Variant Analysis getindels_2way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 1.0.0 numpy True False +gmaj gmaj_1 GMAJ Multiple Alignment Viewer To update Visualization gmaj devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj 2.0.1 True False +hisat hisat HISAT is a fast and sensitive spliced alignment program. To update http://ccb.jhu.edu/software/hisat/index.shtml Assembly hisat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat 1.0.3 hisat True False +indels_3way indels_3way Fetch Indels from 3-way alignments To update Sequence Analysis indels_3way devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way 1.0.3 True False +logistic_regression_vif LogisticRegression Perform Logistic Regression with vif To update Sequence Analysis, Variant Analysis, Statistics logistic_regression_vif devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif 1.0.1 numpy True False +maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file To update Sequence Analysis, Variant Analysis maf_cpg_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 1.0.0 bx-python 0.10.0 True False +mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track To update Visualization, Convert Formats, Next Gen Mappers mapping_to_ucsc devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc 1.0.0 True False +microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths To update Sequence Analysis microsatellite_birthdeath devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath 1.0.0 True False +microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites from pair-wise alignments To update Sequence Analysis, Variant Analysis microsats_alignment_level devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level 1.0.0 sputnik True False +microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes To update Sequence Analysis, Variant Analysis microsats_mutability devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability 1.1.0 bx-python 0.10.0 True False +multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites To update Sequence Analysis, Variant Analysis multispecies_orthologous_microsats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 1.0.0 bx-sputnik True True +quality_filter qualityFilter Filter nucleotides based on quality scores To update Sequence Analysis, Variant Analysis quality_filter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 1.0.1 bx-python 0.10.0 True True +rcve rcve1 Compute RCVE To update Sequence Analysis, Variant Analysis rcve devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve 1.0.0 R True False +short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads To update Sequence Analysis, Graphics short_reads_figure_high_quality_length devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length 1.0.0 rpy True False +short_reads_figure_score quality_score_distribution Build base quality distribution To update Sequence Analysis, Graphics short_reads_figure_score devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score 1.0.2 fontconfig True False +substitution_rates subRate1 Estimate substitution rates for non-coding regions To update Sequence Analysis, Variant Analysis substitution_rates devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 1.0.0 True False +substitutions substitutions1 Fetch substitutions from pairwise alignments To update Sequence Analysis, Variant Analysis substitutions devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 1.0.1 bx-python 0.10.0 True False +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 True False +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 True False +ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser To update Sequence Analysis ucsc_custom_track devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1.0.1 python True False +weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval To update Sequence Analysis, Variant Analysis weightedaverage devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage 1.0.1 galaxy-ops 1.1.0 True False +windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 True False +hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 True False +hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R True False +find_diag_hits find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 True False +gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 True True +kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk True True +lca_wrapper lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 True True +poisson2test poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 True False +t2ps Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 True True +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 True True +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 True False +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 True False +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 True False +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 True False +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 True False +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 True False +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 True False +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 True False +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn True False +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 True False +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust 0.5 graphclust-wrappers 0.6.0 True False +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 True False +antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Up-to-date https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash 6.1.1 antismash 6.1.1 True True +augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 True False +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 True False +barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.0 True False +bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True True +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 True True +crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 True False +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 True True +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 True True +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 True False +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm True True +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 True False +graphclust graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust True False +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 True True +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 True False +homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer True False +illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript True False +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 True False +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 True True +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 True True +labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels True False +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 True True +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 True True +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 True True +methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools True False +methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 True False +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 True False +miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript True False +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 True False +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 True True +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 True False +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 True True +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 True True +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 True False +peakachu peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu 0.2.0+galaxy1 peakachu 0.2.0 True False +pfamscan pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 True True +piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 True False +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus True False +plotly_ml_performance_plots plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas True False +plotly_parallel_coordinates_plot plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python True False +plotly_regression_performance_plots plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python True False +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 True False +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 True False +improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 True False +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 True True +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +compalignp compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ 1.0 compalignp 1.0 True False +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 True False +dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python True False +dorina dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 True False +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 True False +dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna True False +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 True False +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 True False +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 True False +infernal infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs Up-to-date http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal 1.1.4 infernal 1.1.4 True True +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna True False +intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.3.2 intarna 3.3.2 True False +kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker True False +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 True False +mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 True False +mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 True False +nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 True False +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 True False +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 True False +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA 0.1 hmmsearch3.0 True True +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 True False +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 True True +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 True False +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 True False +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ True False +rnabob rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 True False +rnacode rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 True False +rnacommender rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender 0.1.1 sam 3.5 True False +rnalien RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 True False +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 True False +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 True False +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 True False +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 True True +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 True False +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 True False +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 True False +vienna_rna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 True False +sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 True False +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.2 True True +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 True False +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 True True +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 True False +vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt 0.2 vt 2015.11.10 True False +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 True True +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 True False +chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc 0.0.3 biopython 1.70 True False +clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.18 True False +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 True True +count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.18 True False +coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.18 True False +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.20 effectiveT3 1.0.1 True True +fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.6 galaxy_sequence_utils 1.1.5 True False +fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.6 galaxy_sequence_utils 1.1.5 True False +fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 True False +fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.4 galaxy_sequence_utils 1.1.5 True False +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 True False +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 True False +nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 True False +predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.9 True False +protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter True False +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 True False +samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.18 True False +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 True False +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 True False +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 True False +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 True False +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 True False +seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.4 biopython 1.70 True False +seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.16 galaxy_sequence_utils 1.1.5 True False +seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.9 galaxy_sequence_utils 1.1.5 True False +seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.14 biopython 1.70 True False +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 True False +TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN 0.1.0 trimns_vgp 1.0 True False +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 True True +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes Up-to-date https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr 1.0.14 abritamr 1.0.14 True True +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 True True +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 True False +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean 0.16.0 aegean 0.16.0 True False +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 True True +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 True True +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 2.7.22 True False +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 True True +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 True True +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.7.5 anndata 0.6.22 True False +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 True False +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 True False +art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art 2014.11.03.0 art 2016.06.05 True False +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic artic 1.2.3 True True +assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 True False +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 True False +b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc 3.0.5+galaxy0 b2btools 3.0.6 True False +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 True True +bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil bamutil 1.0.15 True False +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 True True +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 True False +barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 True False +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 True False +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 True True +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.01 bbmap 39.01 True False +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 0.2.2 bctools 0.2.2 True False +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 True False +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 True True +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python True False +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 True True +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 True False +biscot biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 True False +blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 True False +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 True True +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 True True +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 True False +calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold 1.0.0 numpy True False +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 True True +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 True True +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 True True +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 True False +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm 1.2.0 checkm-genome 1.2.2 True True +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri 0.7 cherri 0.8 True False +chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 True False +chromeister chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a True False +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 True False +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 True False +clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins " + clustalw + " 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 True True +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 True True +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac 0.9.1 cojac 0.9.1 True True +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread 24.7.14+galaxy0 commet 24.7.14 True False +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 True True +coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report 0.0.4 perl-number-format 1.76 True False +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 True True +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 True False +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 True False +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 True True +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 bioconductor-dada2 1.28.0 True True +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 True True +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 True False +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 True False +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 True False +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 True True +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 True True +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 True True +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis 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 True True +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 True False +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 True False +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 True False +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 True False +exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 True False +exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 True False +export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 True True +fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 True True +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 True False +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 True False +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 True False +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 True True +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 True True +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 True True +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 True False +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 True False +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit r193 fermi2 r193 True False +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 True False +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 True True +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 True False +flash flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 True False +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 True True +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.7 True True +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " + funannotate + " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 True True +gecko gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko 1.2 gecko 1.2 True False +gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini 0.20.1 gemini 0.30.2 True False +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 True False +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 True False +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 True False +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 True False +gffread gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 True False +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base True False +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer glimmer 3.02 True True +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 True True +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 True True +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 True True +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 True True +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 True True +gwastools gwastools_manhattan_plot gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc 0.1.0 bioconductor-gwastools 1.46.0 True False +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 True True +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 True True +hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc 1.3.3 hapcut2 1.3.3 True False +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 True False +heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 3.1.3 r-gplots 2.17.0 True False +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 True False +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 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 True False +hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff 3.1.5 hicstuff 3.2.1 True False +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 True True +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 True False +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 True True +homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer 4.11 homer 4.11 True False +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 True False +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 True True +hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper 2.1.6 hybpiper 2.1.6 True False +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ 2.5.47 hyphy 2.5.50 True True +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 True True +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 True True +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 True True +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 True False +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 True False +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 True True +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 True False +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 True True +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 True True +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 True False +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 True False +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ 1.4.2 ivar 1.4.2 True True +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 True True +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 True False +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 True True +kc-align kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align 1.0.2 kcalign 1.0.2 True True +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer 3.0.0a3 khmer 3.0.0a3 True True +kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 True True +kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 True True +kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 True True +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 True True +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 True True +krocus krocus Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus 1.0.1 krocus 1.0.3 True True +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 True False +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 True True +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 True False +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 True False +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 True True +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 True False +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 True True +m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet 2.1.0 m6anet 2.1.0 True True +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 True True +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 True False +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 True True +mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq 2.1.1 perl True True +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 True True +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 True False +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 True True +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka 1.7.2 medaka 1.11.1 True True +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 True True +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 True True +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.24.20 True True +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype 0.8.5 meningotype 0.8.5 True True +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 True True +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 True True +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 True True +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 True True +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.42.0 True True +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 True True +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 True False +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 True True +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 True True +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 True True +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 True False +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 True False +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 True True +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 True True +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers 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 True True +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 True True +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 True True +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mumer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. Multiple sequence alignment Sequence analysis, Human genetics Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 True False +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe 0.10.0 mykrobe 0.13.0 True True +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ 0.1.2 naltorfs 0.1.2 True False +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 True True +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 True True +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 True True +necat necat Error correction and de-novo assembly for ONT Nanopore reads necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 True False +newick_utils newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 True True +nextclade nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 True True +nonpareil nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 True True +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 True False +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup 2.3.3 nudup 2.3.3 True True +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 True False +odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.3 True False +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.1 True False +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 True False +orfipy orfipy Galaxy wrapper for ORFIPY orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy 0.0.4 orfipy 0.0.4 True True +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis To update https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder 2.5.4 orthofinder 2.5.5 True True +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 True False +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 True False +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 True False +pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes " + pharokka + " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " + pharokka + " True True +phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.44.0 True True +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 True True +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 True True +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 True True +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 True True +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 True True +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 True False +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto 0.6.2 presto 0.7.1 True False +pretext pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext 0.1.9 pretextmap 0.1.9 True False +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 True False +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 True False +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 True True +prot-scriber prot_scriber Protein annotation of short human readable descriptions Up-to-date https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber 0.1.4 prot-scriber 0.1.4 True False +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 True True +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 True False +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 True False +pycoqc pycoqc QC metrics for ONT Basecalling Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc 2.5.2 pycoqc 2.5.2 True True +pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks 3.8 pygenometracks 3.8 True True +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb 1.4.2 pysradb 2.2.0 True False +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 True True +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ qiime 1.9.1 True True +qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc 0.1.0 r-qqman 0.1.4 True False +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management 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 True True +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 True True +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge 0.3 quickmerge 0.3 True True +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 True False +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 True False +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 True False +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 True True +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 True True +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 True True +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 True False +repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 True False +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 True False +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology Up-to-date https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz 1.2.0 ribowaltz 1.2.0 True False +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 True False +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 True True +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 True True +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 True False +salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 2.3 salsa2 2.3 True False +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 True True +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 True True +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ @galaxy_version@ scanpy 1.7.2 True False +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater 1.22.0 bioconductor-scater 1.28.0 True False +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer 4 schicexplorer 7 True False +scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio 0.4.2 scikit-bio 0.4.2 True False +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 True True +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 True False +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 True True +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 True False +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 True False +seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.5.1 True True +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 True False +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 True False +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 True False +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 True False +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah 1.1.3 shorah 1.99.2 True False +shovill shovill Faster de novo assembly pipeline based around Spades shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill 1.1.0 shovill 1.1.0 True True +sickle sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle 1.33.2 sickle-trim 1.33 True False +sina sina SINA reference based multiple sequence alignment sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina 1.7.2 sina 1.7.2 True False +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto 0.9.0 sinto 0.10.0 True False +slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk 0.4.3 slamdunk 0.4.3 True False +sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth 0.30.1 r-sleuth 0.30.1 True False +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 True True +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 True False +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap 2013_11_29 snap 2013_11_29 True True +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 True False +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 True False +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 True True +socru socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru 2.1.7 socru 2.2.4 True False +sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 True True +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades 3.15.5 spades 3.15.5 True True +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 True False +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 True True +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 True True +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks stacks 2.65 True False +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 2.55 stacks 2.65 True False +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 True False +structure structure for using multi-locus genotype data to investigate population structure. structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure 2.3.4 structure 2.3.4 True True +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester 0.6.94 structureharvester 0.6.94 True False +syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA 1.0 clustalo 1.2.4 True False +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 True False +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc 0.3.0 rust-ncbitaxonomy 1.0.7 True False +taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 True True +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler 4.4.1 tb-profiler 5.0.1 True True +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 True False +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 True False +telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope 1.0.3 telescope 1.0.3 True False +tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts 2.2.3 tetranscripts 2.2.3 True False +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 True False +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 True False +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 True False +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 True False +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 True True +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 True False +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 True False +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler 0.5.4 trycycler 0.5.4 True False +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 True False +ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l 377 ucsc-blat 445 True False +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 True False +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 True True +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 True True +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 True True +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 True True +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 True True +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 True True +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser 2.2.6+galaxy2 velvet 1.2.10 True True +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 True False +vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg 1.23.0 vg 1.52.0 True False +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 True False +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 True True +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp 3.0.6 pysam 0.22.0 True False +weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app 0.1.2 curl True False +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 True False +bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 True True +bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 True False +bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 True False +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 True True +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 True True +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 True True +ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 True False +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 True False +blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.6.0 blast 2.14.1 True False +bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 True False +calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp 3.0.13 calisp 3.0.13 True False +cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.2.1 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +data_manager_eggnog_mapper downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager True False +data_manager_eggnog_mapper_abspath download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath True False +eggnog_mapper eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 True True +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +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 True False +maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant 1.22.0 r-base True False +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 True False +maxquant maxquant, maxquant_mqpar wrapper for MaxQuant Up-to-date https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 True False +meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 True False +metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage To update Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator 1.0.0 metagene_annotator 1.0 True True +metanovo metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 True False +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 True False +moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 True False +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 True False +mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.62.1 True False +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 True False +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 True False +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 True False +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 True False +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 True False +mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp 1.1.0 r-tidyverse True False +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 True False +openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 True False +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 True False +pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python True False +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 True False +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 True False +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 True False +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 True False +pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls True False +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 True False +pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools 1.3 python True False +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base True False +custom_pro_db custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 True False +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db True False +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam 1.3.2.1 r-base True False +translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 True False +proteomiqon_joinquantpepionswithproteins proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 True False +proteomiqon_labeledproteinquantification proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 True False +proteomiqon_labelfreeproteinquantification proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 True False +proteomiqon_mzmltomzlite proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 True False +proteomiqon_peptidedb proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 True False +proteomiqon_peptidespectrummatching proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 True False +proteomiqon_proteininference proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 True False +proteomiqon_psmbasedquantification proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 True False +proteomiqon_psmstatistics proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 True False +proteore_venn_diagram proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python True False +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 True False +pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 True False +pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.6.2 True False +quantp quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 True False +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 True False +rawtools rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 True False +sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 True False +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 True False +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 True False +translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 True False +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 True False +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 True False +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 True False +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.0 True False +blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blast_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 1.1.0 python True False +blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits To update http://artbio.fr Assembly, RNA blastparser_and_hits artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits 2.7.1 python True False +blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python True False +cap3 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 True False +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.40.2 True False +fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.32.0 True False +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization 0.9.6 r-optparse 1.3.2 True False +guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy 0.2.1 True False +high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap 1.2.0 r-gplots 2.17.0 True False +mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats 0.19.1+galaxy0 r-optparse 1.3.2 True False +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.5.1 tar True False +oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/oases 1.3.0 oases 0.2.09 True False +probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage 0.7.0 samtools 1.18 True False +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 True False +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot 0.1.1 python True False +small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_clusters artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters 1.3.0 pysam 0.22.0 True False +small_rna_maps small_rna_maps Generates small read maps from alignment BAM files To update http://artbio.fr RNA, SAM, Graphics, Next Gen Mappers small_rna_maps artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps 3.1.1 numpy True False +small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. To update http://artbio.fr RNA small_rna_signatures artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures 3.4.2 pysam 0.22.0 True False +sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads To update http://artbio.fr RNA, Next Gen Mappers sr_bowtie artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie 2.3.0 bowtie 1.3.1 True False +sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. To update http://artbio.fr RNA sr_bowtie_dataset_annotation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation 2.8 bowtie 1.3.1 True False +tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files To update http://artbio.fr Nanopore tarfast5 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 0.6.1 pigz True False +xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing To update https://github.com/GoekeLab/xpore Nanopore xpore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore 2.1+galaxy0 xpore 2.1 True False +yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper 2.5.1 python True False +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 True False +Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base True False +PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy 0.0.2 True True +champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs 0.0.0 r-base True False +consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments 1.0.0 r-bioseq True False +data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools 0.0.0 r-tangles True False +xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ 2022.3.0 xarray True False +gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 True False +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 True True +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 True False +spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 True False +srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools 0.0.1 r-base True False +stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc 0.0.2 True False +vigiechiro vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid Tools created by the vigiechiro team to analyses and identify chiro sounds files. To update https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro Ecology vigiechiro ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro 0.1.1 True False +climate-stripes climate_stripes Create climate stripes from a tabular input file To update https://www.climate-lab-book.ac.uk/2018/warming-stripes/ Climate Analysis, Visualization climate_stripes climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1.0.2 python True False +mean-per-zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file To update https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ Visualization, GIS, Climate Analysis mean_per_zone climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0.2.0 python True False +psy-maps psy_maps Visualization of regular geographical data on a map with psyplot To update https://github.com/Chilipp/psy-maps Visualization, Climate Analysis psy_maps climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps 1.2.1 python True False +droplet-barcode-plot _dropletBarcodePlot Make a cell barcode plot for droplet single-cell RNA-seq QC To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis droplet_barcode_plot ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml 1.6.1+galaxy2 scxa-plots 0.0.1 True False +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 True False +gtf-2-gene-list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis gtf2gene_list ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.0 True False +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 True False +salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary Sequence Analysis salmon_kallisto_mtx_to_10x ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml 0.0.1+galaxy6 scipy True False +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.1.1 cell-types-analysis 0.1.11 True False +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 True False +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ v0.0.2+galaxy2 wget True False +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 True False +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.2.8 garnett-cli 0.0.5 True False +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.1.4 monocle3-cli 0.0.9 True False +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.8.0 sc3-scripts 0.0.6 True False +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy 1.8.1 scanpy-scripts 1.1.6 True False +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.10.0 scater-scripts 0.0.5 True False +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.6.3 scmap-cli 0.0.11 True False +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.2 scpred-cli 0.1.0 True False +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 True False +mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml True False +consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +filter_vcf filtervcf SNVPhyl filter_vcf Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_vcf nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis find_repeats nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis snv_matrix nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy 1.8.2 snvphyl-tools 1.8.2 True False +suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy True False