diff --git a/results/all_tools.tsv b/results/all_tools.tsv index 77b92e05..f0ae4cea 100644 --- a/results/all_tools.tsv +++ b/results/all_tools.tsv @@ -1,4 +1,37 @@ Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 (0/1) (0/1) (0/1) (0/1) +baric_archive baric_archive_rennes, baric_archive_toulouse A data source tool to fetch data from a BARIC Archive server. To update https://www.cesgo.org/catibaric/ Data Source genouest https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive 1.1.0 (0/2) (0/2) (0/2) (2/2) +braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) (0/1) +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 3.0.8 (0/1) (1/1) (1/1) (1/1) +feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 To update https://github.com/tderrien/FEELnc Convert Formats feelnc2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0.1 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor To update Metabolomics gcms2isocor genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +get_pairs get_pairs Separate paired and unpaired reads from two fastq files To update Fastq Manipulation get_pairs genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0.3 python (0/1) (0/1) (0/1) (0/1) +helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks helixer helixer Helixer Deep Learning to predict gene annotations Gene prediction, Genome annotation Sequence analysis, Gene transcripts To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.3 (0/1) (0/1) (1/1) (1/1) +logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) (0/1) +meneco meneco Meneco computes minimal completions to your draft network with reactions from a repair network Up-to-date http://bioasp.github.io/meneco/ Systems Biology meneco genouest https://github.com/genouest/galaxy-tools/tree/master/tools/meneco https://github.com/genouest/galaxy-tools/tree/master/tools/meneco 1.5.2 meneco 1.5.2 (0/1) (0/1) (0/1) (0/1) +miranda2asko miranda2asko Converts miRanda output into AskOmics format To update Convert Formats miranda2asko genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0.2 perl (0/1) (0/1) (0/1) (0/1) +openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." To update Metabolomics openlabcds2csv genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0.1.0 openjdk (0/1) (0/1) (0/1) (0/1) +peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper 2.0 (0/4) (0/4) (0/4) (0/4) +Ensembl-REST get_feature_info, get_genetree, get_sequences A suite of Galaxy tools designed to work with Ensembl REST API. To update https://rest.ensembl.org Data Source earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST 0.1.2 requests (0/3) (0/3) (3/3) (0/3) +GAFA gafa Gene Align and Family Aggregator To update http://aequatus.tgac.ac.uk Visualization gafa earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0.3.1 (0/1) (0/1) (1/1) (0/1) +TreeBest treebest_best TreeBeST best treebest treebest TreeBeST TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetics To update http://treesoft.sourceforge.net/treebest.shtml Phylogenetics treebest_best earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest 1.9.2.post0 treebest 1.9.2.post1 (0/1) (0/1) (1/1) (0/1) +apoc 3.0 1.0 apoc Large-scale structural comparison of protein pockets To update http://cssb.biology.gatech.edu/APoc Computational chemistry apoc earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1.0+galaxy1 apoc 1b16 (1/1) (0/1) (1/1) (0/1) +blast_parser 296.0 27.0 blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics blast_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0.1.2 (0/1) (0/1) (1/1) (0/1) +ete 1255.0 67.0 ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit ete ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org Phylogenetic analysis, Phylogenetic tree editing Phylogenetics To update http://etetoolkit.org/ Phylogenetics ete earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete 3.1.2 ete3 3.1.1 (0/7) (0/7) (7/7) (7/7) +export_to_cluster export_to_cluster Export datasets to cluster To update https://github.com/TGAC/earlham-galaxytools/ Data Export export_to_cluster earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0.0.2 EXPORT_DIR_PREFIX (0/1) (0/1) (0/1) (0/1) +gblocks gblocks Gblocks Up-to-date http://molevol.cmima.csic.es/castresana/Gblocks.html Sequence Analysis gblocks earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0.91b gblocks 0.91b (0/1) (1/1) (0/1) (1/1) +gstf_preparation 397.0 4.0 gstf_preparation GeneSeqToFamily preparation converts data for the workflow To update https://github.com/TGAC/earlham-galaxytools/ Convert Formats gstf_preparation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0.4.3 python (0/1) (0/1) (1/1) (0/1) +hcluster_sg 238.0 13.0 hcluster_sg Hierarchically clustering on a sparse graph To update https://github.com/douglasgscofield/hcluster Phylogenetics hcluster_sg earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0.5.1.1 hcluster_sg 0.5.1 (0/1) (0/1) (1/1) (0/1) +hcluster_sg_parser 290.0 7.0 hcluster_sg_parser Converts hcluster_sg 3-column output into lists of ids To update https://github.com/TGAC/earlham-galaxytools/ Phylogenetics hcluster_sg_parser earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser 0.2.1 (0/1) (0/1) (1/1) (0/1) +lotus2 936.0 114.0 lotus2 LotuS2 OTU processing pipeline lotus2 lotus2 lotus2 LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Sequence feature detection, DNA barcoding Metagenomics, Taxonomy, Microbial ecology Up-to-date http://lotus2.earlham.ac.uk/ Metagenomics lotus2 earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 2.32 lotus2 2.32 (0/1) (0/1) (1/1) (0/1) +miranda 6076.0 41.0 miranda Finds potential target sites for miRNAs in genomic sequences To update http://www.microrna.org/ RNA miranda earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 3.3a+galaxy1 miranda 3.3a (0/1) (0/1) (1/1) (1/1) +plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. To update Computational chemistry plotheatmap earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 1.0 bioconductor-preprocesscore 1.64.0 (0/1) (0/1) (0/1) (0/1) +rdock rdock Docking ligands to proteins and nucleic acids To update http://rdock.sourceforge.net/ Computational chemistry rdock earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 1.0 rDock 2013.1 (0/1) (0/1) (0/1) (0/1) +replace_chromosome_names 537.0 20.0 replace_chromosome_names Replace chromosome names To update Text Manipulation replace_chromosome_names earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0.1 python (0/1) (0/1) (1/1) (0/1) +rsat_filter_snps rsat_filter_snps Filter SNPs in RSAT Matrix Scan output To update https://github.com/TGAC/earlham-galaxytools/ ChIP-seq, Systems Biology rsat_filter_snps earlham https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps 0.1 (0/1) (0/1) (0/1) (0/1) +smart_domains smart_domains SMART domains To update http://smart.embl.de/ Sequence Analysis smart_domains earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) +smina 493.0 9.0 smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization To update https://sourceforge.net/projects/smina/ Computational chemistry smina earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1.0 smina 2017.11.9 (1/1) (0/1) (1/1) (0/1) +t_coffee 8690.0 70.0 t_coffee T-Coffee To update http://www.tcoffee.org/ Sequence Analysis t_coffee earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 13.45.0.4846264 t-coffee 13.46.0.919e8c6b (0/1) (0/1) (1/1) (0/1) abacas abacas Order and Orientate Contigs To update https://github.com/phac-nml/abacas Assembly abacas nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 1.1 mummer 3.23 (0/1) (0/1) (0/1) (1/1) assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) To update https://github.com/phac-nml/galaxy_tools Assembly assemblystats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 1.1.0 perl-bioperl 1.7.8 (0/1) (0/1) (0/1) (0/1) bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. To update https://github.com/phac-nml/galaxy_tools Assembly bam2mappingstats nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 1.1.0 perl (0/1) (0/1) (0/1) (0/1) @@ -79,6 +112,8 @@ tripal analysis_add_analysis, analysis_get_analyses, analysis_load_blast, anal w4mcorcov 368.0 5.0 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov 0.98.18 r-base (0/1) (1/1) (1/1) (0/1) w4mclassfilter 2834.0 3.0 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0.98.19 r-base (0/1) (1/1) (1/1) (0/1) w4mjoinpn 171.0 2.0 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn 0.98.2 coreutils 8.25 (0/1) (1/1) (1/1) (0/1) +ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) +segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. Up-to-date https://github.com/gsneha26/SegAlign Next Gen Mappers segalign richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 0.1.2.1 segalign-full 0.1.2.1 (1/1) (0/1) (0/1) (0/1) suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2023.5.0+q2galaxy.2023.5.0.2 (3/3) (3/3) (3/3) (3/3) suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2023.5.0+q2galaxy.2023.5.0.2 (4/5) (4/5) (4/5) (2/5) suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2023.5.1+q2galaxy.2023.5.0.2 (4/4) (4/4) (4/4) (4/4) @@ -194,7 +229,7 @@ substitutions substitutions1 Fetch substitutions from pairwise alignments t_test_two_samples 210.0 6.0 t_test_two_samples T Test for Two Samples To update Statistics t_test_two_samples devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1.0.1 R (1/1) (1/1) (1/1) (1/1) table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered To update Variant Analysis table_annovar devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0.2 annovar (0/1) (0/1) (0/1) (0/1) tabular_to_fasta 319234.0 601.0 tab2fasta Tabular-to-FASTA To update Convert Formats tabular_to_fasta devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1.1.1 python (1/1) (1/1) (1/1) (1/1) -tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.19.2 (0/1) (0/1) (0/1) (0/1) +tophat 1.0 tophat Tophat for Illumina To update RNA, Next Gen Mappers tophat devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 1.5.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) tophat2 24167.0 312.0 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads To update http://ccb.jhu.edu/software/tophat/index.shtml RNA, Next Gen Mappers tophat2 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 2.1.1 bowtie2 2.5.3 (1/1) (1/1) (1/1) (0/1) tophat_fusion_post 216.0 15.0 tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ (0/1) (1/1) (1/1) (0/1) trimmer 6058.0 188.0 trimmer Trim leading or trailing characters. To update Text Manipulation trimmer devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 0.0.1 (1/1) (1/1) (1/1) (1/1) @@ -233,11 +268,209 @@ t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) (0/1) vcftools_annotate 171.0 24.0 vcftools_annotate Annotate VCF using custom/user-defined annotations To update https://vcftools.github.io/ Variant Analysis vcftools_annotate devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 0.1 echo (1/1) (0/1) (1/1) (1/1) vcftools_compare 531.0 34.0 vcftools_compare Compare VCF files to get overlap and uniqueness statistics To update https://vcftools.github.io/ Variant Analysis vcftools_compare devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) -vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.19.2 (0/1) (0/1) (0/1) (0/1) +vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence To update https://vcftools.github.io/ Variant Analysis vcftools_consensus devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0.1.11 samtools 1.20 (0/1) (0/1) (0/1) (0/1) vcftools_isec 498.0 35.0 vcftools_isec Intersect multiple VCF datasets To update https://vcftools.github.io/ Variant Analysis vcftools_isec devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0.1.1 tabix 1.11 (0/1) (1/1) (1/1) (0/1) vcftools_merge 953.0 68.0 vcftools_merge Merge multiple VCF datasets into a single dataset To update https://vcftools.github.io/ Variant Analysis vcftools_merge devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0.1.11 tabix 1.11 (0/1) (1/1) (1/1) (0/1) vcftools_slice 411.0 24.0 vcftools_slice Subset VCF dataset by genomic regions To update https://vcftools.github.io/ Variant Analysis vcftools_slice devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 0.1 echo (1/1) (0/1) (1/1) (1/1) vcftools_subset 137.0 17.0 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) (0/1) +10x_bamtofastq 228.0 46.0 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) (0/1) +AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResults glob_report Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. To update RNA graphclust_postprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +CollectResultsNoAlign graphclust_glob_report_no_align Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. To update RNA graphclust_postprocessing_no_align rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +GSPAN gspan Second step of GraphClust To update RNA graphclust_fasta_to_gspan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +LocARNAGraphClust locarna_best_subtree MLocARNA computes a multiple sequence-structure alignment of RNA sequences. To update RNA graphclust_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +NSPDK NSPDK_candidateClust, nspdk_sparse Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. To update RNA graphclust_nspdk rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK 9.2.3.1 graphclust-wrappers 0.6.0 (0/2) (0/2) (2/2) (0/2) +Plotting motifFinderPlot Plotting results for GraphClust To update RNA graphclust_motif_finder_plot rnateam https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting 0.4 seaborn (0/1) (0/1) (1/1) (0/1) +PrepareForMlocarna preMloc This tool prepares files for locarna step. To update RNA graphclust_prepocessing_for_mlocarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Preprocessing preproc Preprocessing input for GraphClust To update RNA graphclust_preprocessing rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0.5 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +Structure_GSPAN structure_to_gspan Convert RNA structure to GSPAN graphs To update RNA structure_to_gspan rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) (0/1) +agat 481.0 42.0 agat GTF/GFF analysis toolkit agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics To update https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.4.0 (0/1) (0/1) (1/1) (1/1) +antismash 14596.0 279.0 antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters antismash antismash antiSMASH Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families To update https://antismash.secondarymetabolites.org Sequence Analysis antismash bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash 6.1.1 antismash 7.1.0 (1/1) (1/1) (1/1) (0/1) +atactk_trim_adapters 257.0 26.0 atactk_trim_adapters Trim adapters from paired-end HTS reads. To update https://github.com/ParkerLab/atactk/ Fastq Manipulation atactk_trim_adapters rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0.1.6 atactk 0.1.9 (0/1) (0/1) (1/1) (0/1) +augustus 8864.0 516.0 augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 3.1.0 augustus 3.5.0 (1/1) (1/1) (1/1) (1/1) +bamhash 169.0 15.0 bamhash Hash BAM and FASTQ files to verify data integrity Up-to-date https://github.com/DecodeGenetics/BamHash Sequence Analysis bamhash bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 1.1 bamhash 1.1 (0/1) (0/1) (1/1) (0/1) +barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm To update https://github.com/YeoLab/gscripts RNA, Sequence Analysis barcode_collapse rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0.1.0 pysam 0.22.0 (0/1) (0/1) (0/1) (0/1) +bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Convert from bigWig to bedGraph format To update Convert Formats bigwig_to_bedgraph bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0.1.0 ucsc_tools (0/1) (0/1) (1/1) (0/1) +biomodelsML biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. To update https://www.ebi.ac.uk/biomodels/ Machine Learning biomodels bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 1.1 (0/2) (0/2) (2/2) (0/2) +bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data To update https://bionanogenomics.com/ Assembly bionano bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 3.7.0 (1/1) (1/1) (1/1) (0/1) +bismark 13575.0 404.0 bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states To update https://www.bioinformatics.babraham.ac.uk/projects/bismark/ Sequence Analysis, Next Gen Mappers bismark bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0.22.1 bismark 0.24.2 (0/4) (4/4) (4/4) (4/4) +blobtoolkit 685.0 21.0 blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. To update https://blobtoolkit.genomehubs.org/ Sequence Analysis, Assembly blobtoolkit bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 4.0.7 (0/1) (1/1) (1/1) (0/1) +blockbuster 3009.0 34.0 blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. To update http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html RNA, Sequence Analysis blockbuster rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 0.1.2 blockbuster 0.0.1.1 (1/1) (1/1) (1/1) (0/1) +canu 13021.0 533.0 canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. De-novo assembly Genomics Up-to-date https://github.com/marbl/canu canu bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu 2.2 canu 2.2 (0/1) (1/1) (1/1) (1/1) +cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.1 (0/1) (0/1) (1/1) (0/1) +cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) +cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) +chipseeker 15690.0 418.0 chipseeker A tool for ChIP peak annotation and visualization To update https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html ChIP-seq, Genome annotation chipseeker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1.32.0 bioconductor-chipseeker 1.38.0 (1/1) (1/1) (1/1) (0/1) +circexplorer 251.0 8.0 circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) To update https://github.com/YangLab/CIRCexplorer Sequence Analysis, RNA circexplorer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 1.1.9.0 circexplorer 1.1.10 (0/1) (1/1) (1/1) (0/1) +combine_metaphlan_humann combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances combine_metaphlan_and_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs Aggregation Metagenomics, Molecular interactions, pathways and networks To update Metagenomics combine_metaphlan2_humann2 bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann 0.3.0 python (0/1) (0/1) (1/1) (0/1) +compare_humann2_output 332.0 10.0 compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information compare_humann2_outputs compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples Comparison Metagenomics, Gene and protein families To update Metagenomics compare_humann2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output 0.2.0 (0/1) (0/1) (0/1) (0/1) +cpat 134.0 21.0 cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 (1/1) (1/1) (1/1) (1/1) +crt crispr_recognition_tool CRISPR Recognition Tool To update Sequence Analysis crispr_recognition_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 1.2.0 crisper_recognition_tool 1.2 (0/1) (0/1) (1/1) (0/1) +diff 235.0 30.0 diff GNU diff tool that calculates the differences between two files. To update http://www.gnu.org/software/diffutils/ Text Manipulation diff bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 3.7 diffutils (1/1) (0/1) (1/1) (0/1) +diffbind 6264.0 250.0 Diffbind provides functions for processing ChIP-Seq data. To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind (0/1) (0/1) (0/1) (0/1) +edta 484.0 58.0 edta The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. edta edta The Extensive de novo TE Annotator (EDTA) The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. De-novo assembly, Deisotoping, Genome annotation Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms To update https://github.com/oushujun/EDTA Variant Analysis edta bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta https://github.com/bgruening/galaxytools/tree/master/tools/edta edta 2.2.0 (0/1) (0/1) (1/1) (0/1) +epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. To update https://github.com/lamortenera/epicseg Epigenetics epicseg rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg @VERSION_STRING@ epicseg 1.0 (0/1) (0/1) (1/1) (0/1) +fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) (0/1) +file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) (1/1) +find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 0.3 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Flye Flye Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Up-to-date https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.3 (1/1) (1/1) (1/1) (1/1) +footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) (0/1) +format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 1.0.0+galaxy1 (0/1) (0/1) (1/1) (0/1) +format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output 0.2.0 (0/1) (0/1) (1/1) (0/1) +gfastats 8159.0 418.0 gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. Data handling Computational biology Up-to-date https://github.com/vgl-hub/gfastats Sequence Analysis gfastats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats 1.3.6 gfastats 1.3.6 (1/1) (1/1) (1/1) (0/1) +glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) To update https://ccb.jhu.edu/software/glimmerhmm/ Sequence Analysis glimmer_hmm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm (0/1) (0/1) (0/1) (0/1) +gotohscan 71.0 1.0 rbc_gotohscan Find subsequences in db To update Sequence Analysis gotohscan rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 1.3.0 gotohscan 1.3 (0/1) (0/1) (1/1) (0/1) +graph_converter graph_converter Convert between different graph formats To update Convert Formats graph_converter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter 0.1.0 (0/1) (0/1) (0/1) (0/1) +graphclust 6.0 graphclust GraphClust can be used for structural clustering of RNA sequences. To update http://www.bioinf.uni-freiburg.de/Software/GraphClust/ RNA graphclust bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphclust https://github.com/bgruening/galaxytools/tree/master/tools/graphclust 0.1 GraphClust (0/1) (0/1) (0/1) (0/1) +graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing To update https://github.com/isovic/graphmap/ Assembly graphmap bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap 0.5.2 graphmap 0.6.3 (0/2) (0/2) (2/2) (0/2) +hclust2 hclust2 Plots heatmaps To update https://bitbucket.org/nsegata/hclust2/ Data Visualization hclust2 rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0.99 hclust2 1.0.0 (0/1) (0/1) (0/1) (0/1) +hictk hictk Convert cooler to juicebox_hic To update https://github.com/paulsengroup/hictk Convert Formats, Epigenetics hictk bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0.0.8 hictk 0.0.12 (0/1) (0/1) (1/1) (0/1) +hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. To update https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html Epigenetics hicup bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 0.9.2 (7/7) (0/7) (7/7) (0/7) +hifiasm 1410.0 297.0 hifiasm A fast haplotype-resolved de novo assembler Up-to-date https://github.com/chhylp123/hifiasm Assembly hifiasm bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm 0.19.8 hifiasm 0.19.8 (1/1) (1/1) (1/1) (1/1) +homer Software for motif discovery and next generation sequencing analysis. To update http://homer.salk.edu/homer/ Sequence Analysis homer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer (0/1) (0/1) (0/1) (0/1) +illumina_methylation_analyser illumina_methylation_analyser Methylation analyzer for Illumina 450k DNA emthylation microarrays To update https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser Sequence Analysis illumina_methylation_analyser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser 0.1 Rscript (0/1) (0/1) (0/1) (0/1) +bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) +graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.43 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) +imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) (0/27) +woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 (0/1) (0/1) (1/1) (0/1) +instagraal 139.0 14.0 instagraal Large genome reassembly based on Hi-C data instagraal instagraal instaGRAAL Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) Genome assembly, Mapping assembly, Genetic mapping, Scaffolding Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites To update https://github.com/koszullab/instaGRAAL Assembly instagraal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/instagraal https://github.com/bgruening/galaxytools/tree/master/tools/instagraal 0.1.6 (0/1) (0/1) (1/1) (0/1) +iprscan5 Interproscan queries the interpro database and provides annotations. To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis iprscan5 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 (0/1) (0/1) (0/1) (0/1) +itsx 868.0 38.0 itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. ITSx ITSx ITSx TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Up-to-date https://microbiology.se/software/itsx/ Metagenomics itsx bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx 1.1.3 itsx 1.1.3 (0/1) (0/1) (1/1) (0/1) +jupyter_job run_jupyter_job Run jupyter notebook script in Galaxy To update Machine Learning run_jupyter_job bgruening https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job 0.0.1 (0/1) (0/1) (0/1) (0/1) +labels bg_labels remaps and annotates alignments To update https://github.com/bgruening/galaxytools/tree/master/tools/labels Sequence Analysis labels bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels (0/1) (0/1) (0/1) (0/1) +lighter 152.0 9.0 lighter Lighter is a kmer-based error correction method for whole genome sequencing data lighter lighter Lighter Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection Sequencing, Whole genome sequencing, DNA, Genomics To update https://github.com/mourisl/Lighter Sequence Analysis, Fasta Manipulation lighter bgruening https://github.com/bgruening/galaxytools/tree/master/tools/lighter https://github.com/bgruening/galaxytools/tree/master/tools/lighter 1.0 lighter 1.1.2 (0/1) (0/1) (1/1) (0/1) +mafft 143045.0 817.0 rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences MAFFT MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Multiple sequence alignment Sequence analysis To update https://mafft.cbrc.jp/alignment/software/ RNA mafft rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft 7.520 mafft 7.525 (2/2) (2/2) (2/2) (2/2) +mavedb mavedb_importer data source for MaveDB To update Data Source mavedb_importer bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0.9 (0/1) (0/1) (1/1) (0/1) +methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis To update https://github.com/bgruening/galaxytools/tree/master/tools/methtools Sequence Analysis methtools bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools (0/8) (0/8) (0/8) (0/8) +methyldackel pileometh A tool for processing bisulfite sequencing alignments To update https://github.com/dpryan79/MethylDackel Sequence Analysis pileometh bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 0.5.2 methyldackel 0.6.1 (1/1) (1/1) (1/1) (0/1) +methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. To update http://bioconductor.org/packages/release/bioc/html/methylKit.html Epigenetics methylkit rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0.99.2 bioconductor-methylkit 1.28.0 (0/1) (0/1) (0/1) (1/1) +metilene 3966.0 103.0 metilene Differential DNA methylation calling To update RNA, Statistics metilene rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 0.2.6.1 metilene 0.2.8 (1/1) (1/1) (1/1) (1/1) +miclip mi_clip Identification of binding sites in CLIP-Seq data. To update https://cran.r-project.org/src/contrib/Archive/MiClip/ Sequence Analysis miclip bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 1.2.0 Rscript (0/1) (0/1) (0/1) (0/1) +minced 895.0 53.0 minced MinCED - Mining CRISPRs in Environmental Datasets To update http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README Sequence Analysis minced bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0.2.0 minced 0.4.2 (0/1) (0/1) (1/1) (0/1) +minipolish 185.0 21.0 minipolish Polishing miniasm assemblies minipolish minipolish minipolish A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. Localised reassembly, Read depth analysis Sequence assembly, Sequencing Up-to-date https://github.com/rrwick/Minipolish Sequence Analysis minipolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish 0.1.3 minipolish 0.1.3 (0/1) (0/1) (1/1) (0/1) +mitohifi 613.0 56.0 mitohifi Assembly mitogenomes from Pacbio HiFi read. To update https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 Assembly mitohifi bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 3 (1/1) (1/1) (1/1) (0/1) +molecule2gspan bg_mol2gspan converter To update https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan Convert Formats molecule_to_gspan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +music_deconvolution 530.0 67.0 music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 (5/5) (5/5) (4/5) (0/5) +nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. Up-to-date https://github.com/jts/nanopolish nanopolish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0.14.0 nanopolish 0.14.0 (0/4) (4/4) (4/4) (4/4) +netboxr 11.0 5.0 netboxr netboxr enables automated discovery of biological process modules by network analysis To update Systems Biology netboxr bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 1.6.0 bioconductor-netboxr 1.9.0 (0/1) (0/1) (1/1) (0/1) +nextdenovo 268.0 84.0 nextdenovo String graph-based de novo assembler for long reads nextdenovo nextdenovo NextDenovo "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages." De-novo assembly, Genome assembly Sequencing, Sequence assembly To update https://github.com/Nextomics/NextDenovo Assembly nextdenovo bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo 2.5.0 nextdenovo 2.5.2 (0/1) (0/1) (1/1) (0/1) +nucleosome_prediction 861.0 2.0 Nucleosome Prediction of Nucleosomes Positions on the Genome nucleosome_prediction nucleosome_prediction nucleosome_prediction Prediction of Nucleosomes Positions on the Genome Prediction and recognition, Nucleosome position prediction, Sequence analysis Structural genomics, Nucleic acid sites, features and motifs Up-to-date https://genie.weizmann.ac.il/software/nucleo_exe.html Sequence Analysis nucleosome_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction 3.0 nucleosome_prediction 3.0 (0/1) (0/1) (1/1) (0/1) +numeric_clustering 486.0 numeric_clustering Clustering tool for numberic values To update http://scikit-learn.org/stable/index.html Statistics numeric_clustering bgruening https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering 0.9 anaconda (0/1) (0/1) (0/1) (1/1) +openms AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter OpenMS in version 2.1. To update Proteomics openms bgruening https://github.com/bgruening/galaxytools/tree/master/tools/openms https://github.com/bgruening/galaxytools/tree/master/tools/openms 2.1.0 openms 3.1.0 (7/140) (34/140) (135/140) (0/140) +pandas_rolling_window 269.0 7.0 pandas_rolling_window Rolling window calculations To update https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html Statistics pandas_rolling_window bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window 0.1 numpy (1/1) (0/1) (1/1) (0/1) +peakachu 3109.0 78.0 peakachu PEAKachu is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA peakachu rnateam https://github.com/tbischler/PEAKachu https://github.com/bgruening/galaxytools/tree/master/tools/peakachu 0.2.0+galaxy1 peakachu 0.2.0 (0/1) (0/1) (1/1) (0/1) +perf stats_perf_tool suitable for boolean classification problems To update http://osmot.cs.cornell.edu/kddcup/software.html stats_perf_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 5.11.0 perf (0/1) (0/1) (0/1) (0/1) +pfamscan 165.0 19.0 pfamscan Search a FASTA sequence against a library of Pfam HMM. pfamscan pfamscan PfamScan This tool is used to search a FASTA sequence against a library of Pfam HMM. Protein sequence analysis Sequence analysis Up-to-date http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Sequence Analysis pfamscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan 1.6 pfam_scan 1.6 (1/1) (1/1) (1/1) (1/1) +pg_tools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history To update https://www.postgresql.org Data Export, Data Source pgtools bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools postgresql (0/3) (0/3) (0/3) (0/3) +pharmcat 82.0 14.0 pharmcat Pharmacogenomics Clinical Annotation Tool To update https://pharmcat.org/ Variant Analysis pharmcat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat (1/1) (0/1) (1/1) (0/1) +piranha 1809.0 39.0 piranha Piranha is a peak-caller for CLIP- and RIP-Seq data To update Sequence Analysis, RNA piranha rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 1.2.1.0 piranha 1.2.1 (0/1) (0/1) (1/1) (0/1) +platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data To update http://www.well.ox.ac.uk/platypus Sequence Analysis platypus bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0.0.11 platypus (0/1) (0/1) (0/1) (0/1) +plotly_ml_performance_plots 1323.0 71.0 plotly_ml_performance_plots performance plots for machine learning problems To update http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics Visualization plotly_ml_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots 0.2 pandas (1/1) (1/1) (1/1) (0/1) +plotly_parallel_coordinates_plot 652.0 37.0 plotly_parallel_coordinates_plot parallel coordinates plot produced with plotly To update https://plot.ly/python/parallel-coordinates-plot/ Visualization plotly_parallel_coordinates_plot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot 0.2 python (1/1) (1/1) (1/1) (0/1) +plotly_regression_performance_plots 843.0 79.0 plotly_regression_performance_plots performance plots for regression problems To update http://scikit-learn.org/stable/supervised_learning.html#supervised-learning Visualization plotly_regression_performance_plots bgruening https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots 0.1 python (1/1) (1/1) (1/1) (0/1) +protease_prediction 149.0 4.0 eden_protease_prediction This tool can learn the cleavage specificity of a given class of proteases. To update https://github.com/fabriziocosta/eden Sequence Analysis, Proteomics protease_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction 0.9 eden 2.0 (0/1) (0/1) (1/1) (0/1) +protein_properties 256.0 15.0 bg_protein_properties Calculation of various properties from given protein sequences To update Sequence Analysis protein_properties bgruening https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +improviser proteomics_improviser Visualisation of PepXML files To update http://www.improviser.uni-freiburg.de/ Proteomics proteomics_improviser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 1.1.0.1 (0/1) (0/1) (0/1) (0/1) +racon 21353.0 309.0 racon Consensus module for raw de novo DNA assembly of long uncorrected reads. Racon Racon Racon Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Up-to-date https://github.com/isovic/racon Sequence Analysis racon bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon 1.5.0 racon 1.5.0 (1/1) (1/1) (1/1) (1/1) +repeat_masker 3750.0 248.0 repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. To update http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 0.1.2 RepeatMasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +replaceColumn replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. To update Text Manipulation replace_column_by_key_value_file bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 0.2 (1/1) (1/1) (1/1) (1/1) +rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. To update https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html Data Source pubchem_rest_tool bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0.1.0 (0/1) (0/1) (0/1) (0/1) +antarna 52.0 2.0 antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . To update RNA antarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 1.1 antarna 2.0.1.2 (0/1) (0/1) (1/1) (0/1) +aresite2 65.0 4.0 AREsite2_REST AREsite2 REST Interface To update http://rna.tbi.univie.ac.at/AREsite RNA, Data Source, Sequence Analysis aresite2 rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0.1.2 python (0/1) (0/1) (1/1) (0/1) +blockclust 1478.0 15.0 blockclust BlockClust detects transcripts with similar processing patterns. Up-to-date https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust RNA blockclust rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1.1.1 blockclust 1.1.1 (1/1) (1/1) (1/1) (0/1) +cmsearch_deoverlap 102.0 1.0 cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. cmsearch-deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results. Comparison, Alignment Biology, Medicine To update https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl RNA cmsearch_deoverlap rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap 0.08+galaxy2 perl (0/1) (0/1) (1/1) (0/1) +cmv 70.0 1.0 cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. Up-to-date https://github.com/eggzilla/cmv RNA cmv rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 1.0.8 cmv 1.0.8 (0/4) (0/4) (2/4) (0/4) +cofold 342.0 8.0 cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. To update http://www.e-rna.org/cofold/ RNA cofold rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 2.0.4.0 cofold 2.0.4 (0/1) (0/1) (1/1) (0/1) +compalignp 220.0 compalignp Compute fractional identity between trusted alignment and test alignment Up-to-date RNA, Sequence Analysis compalignp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 1.0 compalignp 1.0 (0/1) (0/1) (1/1) (0/1) +coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) (0/1) +dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) (0/1) +dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 1.0 (0/1) (0/1) (1/1) (0/1) +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 (0/1) (0/1) (0/1) (0/1) +dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) (0/1) +exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) (0/1) +graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) (0/1) +htseq-clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets To update https://github.com/EMBL-Hentze-group/htseq-clip Sequence Analysis, RNA, CLIP-seq htseq_clip rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 (0/1) (0/1) (1/1) (0/1) +infernal 100230.0 67.0 infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities." infernal infernal Infernal "Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence." Nucleic acid feature detection Sequence sites, features and motifs, Structural genomics To update http://infernal.janelia.org/ RNA infernal bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal 1.1.4 infernal 1.1.5 (0/6) (6/6) (6/6) (0/6) +inforna INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. To update http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp RNA inforna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna (0/1) (0/1) (0/1) (0/1) +intarna 7569.0 23.0 intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.4.0 intarna 3.4.0 (0/1) (0/1) (1/1) (0/1) +kinwalker 70.0 3.0 Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker (0/1) (0/1) (0/1) (0/1) +locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 (0/5) (0/5) (1/5) (0/5) +mea 85.0 3.0 mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 (0/1) (0/1) (1/1) (0/1) +mqc 76.0 5.0 mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 1.9 mqc 1.10 (0/1) (0/1) (1/1) (0/1) +nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 (0/1) (0/1) (1/1) (0/1) +paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) (0/1) +pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) (0/1) +rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) +rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) +rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) (0/1) +reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (0/1) (0/1) +remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) (0/1) +ribotaper 628.0 44.0 ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. Gene expression profiling Functional genomics To update https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ RNA ribotaper rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper 1.3.1a ribotaper 1.3.1 (0/3) (0/3) (3/3) (0/3) +rna_shapes RNAshapes Compute secondary structures of RNA To update RNA rnashapes rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes 3.3.0 @EXECUTABLE@ (0/1) (0/1) (1/1) (0/1) +rnabob 164.0 3.0 rbc_rnabob Fast pattern searching for RNA structural motifs To update http://eddylab.org/software.html RNA rnabob rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob 2.2.1.0 rnabob 2.2.1 (0/1) (0/1) (1/1) (0/1) +rnacode 1358.0 5.0 rbc_rnacode Analyze the protein coding potential in MSA To update RNA rnacode rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode 0.3.2 rnacode 0.3 (0/1) (0/1) (1/1) (0/1) +rnacommender 1074.0 6.0 rbc_rnacommender RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. To update https://github.com/gianlucacorrado/RNAcommender RNA rnacommender rnateam https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender 0.1.1 sam 3.5 (0/1) (0/1) (1/1) (0/1) +rnalien 33.0 4.0 RNAlien RNAlien unsupervized RNA family model construction To update http://rna.tbi.univie.ac.at/rnalien/ RNA, Sequence Analysis rnalien rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien 1.3.6 rnalien 1.8.0 (0/1) (0/1) (1/1) (0/1) +rnasnp 86.0 5.0 rnasnp RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs To update http://rth.dk/resources/rnasnp/ RNA rnasnp rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp 1.2.0 rnasnp 1.2 (0/1) (0/1) (1/1) (0/1) +rnaz 42965.0 14.0 rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. Up-to-date https://www.tbi.univie.ac.at/~wash/RNAz/ RNA rnaz bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz 2.1.1 rnaz 2.1.1 (0/6) (0/6) (6/6) (0/6) +selectsequencesfrommsa 457.0 27.0 selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format Up-to-date https://github.com/eggzilla/SelectSequences RNA, Sequence Analysis selectsequencesfrommsa rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 1.0.5 selectsequencesfrommsa 1.0.5 (0/1) (0/1) (1/1) (0/1) +sortmerna 18504.0 376.0 bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Sequence similarity search, Sequence comparison, Sequence alignment analysis Metatranscriptomics, Metagenomics Up-to-date http://bioinfo.lifl.fr/RNA/sortmerna/ RNA sortmerna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna 4.3.6 sortmerna 4.3.6 (1/1) (1/1) (1/1) (1/1) +sshmm 223.0 5.0 sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data Up-to-date https://github.molgen.mpg.de/heller/ssHMM Sequence Analysis, RNA sshmm rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 1.0.7 sshmm 1.0.7 (0/1) (0/1) (1/1) (0/1) +targetfinder 713.0 37.0 targetfinder Plant small RNA target prediction tool Up-to-date https://github.com/carringtonlab/TargetFinder.git RNA targetfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1.7 targetfinder 1.7 (1/1) (1/1) (1/1) (0/1) +trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. To update http://mbioserv2.mbioekol.lu.se/ARAGORN/ RNA trna_prediction bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0.6 aragorn 1.2.41 (0/2) (2/2) (2/2) (0/2) +vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) (0/23) +sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) (1/1) +salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) +sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_slice, sambamba_sort, sambamba_view, sambamba_depth SAMBAMBA: process your BAM data faster! To update https://github.com/lomereiter/sambamba SAM sambamba rnateam https://github.com/bgruening/galaxytools/tree/master/tools/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba sambamba 1.0 (0/7) (0/7) (0/7) (0/7) +sed sed_stream_editor Manipulate your data with the sed command line tool. To update https://github.com/bgruening/galaxytools/tree/master/tools/sed Text Manipulation sed_wrapper bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed (0/1) (0/1) (0/1) (0/1) +segemehl 1276.0 30.0 segemehl segemehl - short read mapping with gaps To update http://www.bioinf.uni-leipzig.de/Software/segemehl/ Next Gen Mappers segemehl rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0.2.0.4 segemehl 0.3.4 (0/1) (0/1) (1/1) (0/1) +sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn To update http://scikit-learn.org Machine Learning, Statistics sklearn bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 1.0.11.0 (30/33) (14/33) (31/33) (16/33) +splitfasta 1295.0 96.0 rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences To update Text Manipulation splitfasta rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 0.4.0 biopython 1.70 (1/1) (0/1) (1/1) (0/1) +statistics bg_statistical_hypothesis_testing Tool for computing statistical tests. To update https://github.com/bgruening/galaxytools/tree/master/tools/statistics Statistics bg_statistical_hypothesis_testing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy (0/1) (0/1) (1/1) (0/1) +stress_ng 47.0 stress_ng stress test a computer system in various selectable ways To update Web Services stress_ng bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0.12.04 stress-ng (0/1) (0/1) (0/1) (0/1) +tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) +add_line_to_file 14480.0 193.0 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange by header name To update Text Manipulation column_arrange_by_header bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 0.2 (1/1) (1/1) (1/1) (1/1) +join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1) (1/1) +split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1) (1/1) +split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.1 python (1/1) (1/1) (1/1) (1/1) +text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 (20/20) (20/20) (20/20) (20/20) +tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) (0/1) +tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1) (0/1) +trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) +uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.4 requests (1/1) (1/1) (1/1) (0/1) +vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. To update Sequence Analysis, Variant Analysis vt bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0.2 vt 2015.11.10 (0/1) (0/1) (0/1) (0/1) +wtdbg 1660.0 116.0 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) (1/1) +align_back_trans 329.0 11.0 align_back_trans Thread nucleotides onto a protein alignment (back-translation) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans Fasta Manipulation, Sequence Analysis align_back_trans peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython To update Graphics, Sequence Analysis, Visualization chromosome_diagram peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0.0.3 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio To update https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell Assembly, Next Gen Mappers, SAM clc_assembly_cell peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.20 (0/2) (0/2) (0/2) (0/2) +clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins clinod clinod clinod The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. Nucleic acid sequence analysis Sequence analysis To update http://www.compbio.dundee.ac.uk/www-nod/ Sequence Analysis clinod peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod 0.1.0 clinod 1.3 (1/1) (0/1) (0/1) (0/1) +count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants Assembly, SAM count_roi_variants peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth To update https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats Assembly, SAM coverage_stats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +effectiveT3 effectiveT3 Find bacterial type III effectors in protein sequences effectivet3 effectivet3 EffectiveT3 Prediction of putative Type-III secreted proteins. Sequence classification Sequence analysis To update http://effectors.org Sequence Analysis effectivet3 peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 0.0.21 effectiveT3 1.0.1 (0/1) (0/1) (0/1) (0/1) +fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation fasta_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id Fastq Manipulation, Sequence Analysis, Text Manipulation fastq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_pair_names fastq_pair_names Extract FASTQ paired read names To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names Sequence Analysis fastq_pair_names peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads To update https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired Sequence Analysis, Text Manipulation fastq_paired_unpaired peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +get_orfs_or_cdss 7.0 get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Sequence Analysis get_orfs_or_cdss peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 (0/1) (1/1) (1/1) (1/1) +mummer 652.0 83.0 mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot To update http://mummer.sourceforge.net/ Graphics, Sequence Analysis, Visualization mummer peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 0.0.8 ghostscript 9.18 (1/1) (0/1) (1/1) (0/1) +nlstradamus nlstradamus Find nuclear localization signals (NLSs) in protein sequences To update http://www.moseslab.csb.utoronto.ca/NLStradamus Fasta Manipulation, Sequence Analysis nlstradamus peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus 0.0.11 NLStradamus 1.8 (0/1) (0/1) (0/1) (0/1) +predictnls predictnls Python reimplementation of predictNLS for Galaxy To update https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls Sequence Analysis predictnls peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls 0.0.10 (0/1) (0/1) (0/1) (0/1) +protein_analysis promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb To update https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis Sequence Analysis tmhmm_and_signalp peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter (0/6) (0/6) (6/6) (0/6) +sample_seqs 3765.0 149.0 sample_seqs Sub-sample sequences files (e.g. to reduce coverage) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis sample_seqs peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) To update http://www.htslib.org/ Assembly, SAM, Sequence Analysis samtools_depad peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0.0.5 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +samtools_depth 4948.0 296.0 samtools_depth Coverage depth via samtools To update http://www.htslib.org/ Assembly, Sequence Analysis, SAM samtools_depth peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 0.0.3 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +samtools_idxstats 48426.0 1450.0 samtools_idxstats BAM mapping statistics (using samtools idxstats) To update http://www.htslib.org/ Assembly, Next Gen Mappers, SAM samtools_idxstats peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 0.0.6 samtools 1.20 (1/1) (1/1) (1/1) (1/1) +seq_composition 874.0 71.0 seq_composition Sequence composition To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition Sequence Analysis seq_composition peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 (1/1) (0/1) (1/1) (1/1) +seq_filter_by_id 25302.0 306.0 seq_filter_by_id Filter sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_filter_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 (1/1) (1/1) (1/1) (1/1) +seq_filter_by_mapping 3784.0 82.0 seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis seq_filter_by_mapping peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length Fasta Manipulation, Fastq Manipulation, Sequence Analysis seq_length peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 (0/1) (0/1) (0/1) (0/1) +seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip Assembly, Fasta Manipulation, Text Manipulation seq_primer_clip peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) +seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) (0/1) +venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) (1/1) suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2023.5.0+q2galaxy.2023.5.0.2 (3/3) (3/3) (3/3) (3/3) suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2023.5.0+q2galaxy.2023.5.0.2 (4/5) (4/5) (4/5) (2/5) suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2023.5.1+q2galaxy.2023.5.0.2 (4/4) (4/4) (4/4) (4/4) @@ -262,6 +495,602 @@ suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiim suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2023.5.0+dist.h193f7cc9.2 (2/2) (2/2) (2/2) (2/2) suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) (0/1) +abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) +abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) +abyss 4278.0 391.0 abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler abyss abyss ABySS De novo genome sequence assembler using short reads. Genome assembly, De-novo assembly, Scaffolding Sequence assembly Up-to-date http://www.bcgsc.ca/platform/bioinfo/software/abyss Assembly abyss iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss 2.3.7 abyss 2.3.7 (0/1) (1/1) (1/1) (0/1) +adapter_removal 217.0 37.0 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) (0/1) +add_input_name_as_column 83150.0 91.0 addName Add input name as column on an existing tabular file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column Text Manipulation add_input_name_as_column mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 0.2.0 python (1/1) (0/1) (1/1) (0/1) +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 (1/4) (4/4) (4/4) (4/4) +aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) (0/1) +allegro allegro Linkage and haplotype analysis from deCODE allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA To update http://www.decode.com/software/ Variant Analysis allegro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro @VER@.0 allegro 3 (0/1) (0/1) (0/1) (0/1) +amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) (0/1) +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 2.8.6 (0/19) (0/19) (19/19) (0/19) +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) (0/1) +ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics, Taxonomy To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) (0/1) +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.3 anndata 0.6.22.post1 (5/5) (4/5) (5/5) (0/5) +annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) (1/1) +arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) (0/3) +art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (0/3) (0/3) +artic artic_guppyplex, artic_minion The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore Sequence alignment Genomics To update https://github.com/artic-network/fieldbioinformatics Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic 1.2.4 (0/2) (0/2) (2/2) (0/2) +assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) (1/1) +augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) (2/2) +b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) (0/1) +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta 1.9.2 bakta 1.9.3 (0/1) (1/1) (1/1) (1/1) +bam_to_scidx 128.0 4.0 bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx Convert Formats bam_to_scidx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) (0/2) +bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) (2/2) +barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes To update https://bitbucket.org/princeton_genomics/barcode_splitter/ Fastq Manipulation barcode_splitter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0.18.4.0 barcode_splitter 0.18.6 (0/1) (0/1) (0/1) (0/1) +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 (4/4) (0/4) (4/4) (0/4) +barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) (1/1) +basil 266.0 35.0 basil Breakpoint detection, including large insertions Up-to-date https://github.com/seqan/anise_basil Variant Analysis basil iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1.2.0 anise_basil 1.2.0 (1/1) (0/1) (1/1) (0/1) +bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) (0/1) +bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) (0/1) +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) (0/6) +bcftools 524.0 78.0 bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment To update https://samtools.github.io/bcftools/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools 1.15.1 bcftools 1.20 (0/5) (0/5) (0/5) (0/5) +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) (0/7) +beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). ga4gh_beacon ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Up-to-date https://github.com/EGA-archive/beacon2-ri-tools/tree/main Variant Analysis beacon2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 2.0.0 beacon2-ri-tools 2.0.0 (0/3) (0/3) (3/3) (0/3) +beagle 54.0 10.0 beagle Beagle is a program for phasing and imputing missing genotypes. To update https://faculty.washington.edu/browning/beagle/beagle.html Variant Analysis beagle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 5.2_21Apr21.304 beagle 5.4_22Jul22.46e (0/1) (0/1) (1/1) (0/1) +bedops bedops-sort-bed BEDOPS: high-performance genomic feature operations Up-to-date https://bedops.readthedocs.io/en/latest/ Genomic Interval Operations bedops_sortbed iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 2.4.41 bedops 2.4.41 (1/1) (0/1) (1/1) (0/1) +bedtools 936832.0 6318.0 bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. Mapping Genomics To update https://github.com/arq5x/bedtools2 Genomic Interval Operations, Text Manipulation bedtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools 2.30.0 bedtools 2.31.1 (37/37) (37/37) (37/37) (37/37) +bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) (0/1) +berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. Up-to-date https://github.com/tseemann/berokka Fasta Manipulation berokka iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0.2.3 berokka 0.2.3 (0/1) (1/1) (0/1) (0/1) +bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF Up-to-date https://github.com/medema-group/BiG-SCAPE Metagenomics bigscape iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape 1.1.9 bigscape 1.1.9 (0/1) (0/1) (1/1) (0/1) +binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) (0/1) +bioext bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! Up-to-date https://pypi.python.org/pypi/biopython-extensions/ Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 0.21.2 python-bioext 0.21.2 (2/2) (0/2) (2/2) (0/2) +bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 0.1.0 python (1/1) (0/1) (1/1) (0/1) +biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. biomformat biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." Formatting Laboratory information management, Sequence analysis To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) (0/6) +bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) (1/1) +biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) (0/1) +blast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome Up-to-date https://ncbi.github.io/magicblast/ Next Gen Mappers magicblast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 1.7.0 magicblast 1.7.0 (0/1) (0/1) (1/1) (0/1) +blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (0/1) +bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping Up-to-date http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.3 (1/1) (1/1) (1/1) (1/1) +bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (0/1) (1/1) (1/1) (1/1) +breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.38.3 (0/1) (1/1) (1/1) (0/1) +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) +bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping To update http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.17 bwa 0.7.18 (2/2) (2/2) (2/2) (2/2) +bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) (1/1) +bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) +cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) +calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) (0/1) +calculate_numeric_param 1393.0 8.0 calculate_numeric_param Calculate a numeric parameter value using integer and float values. To update Text Manipulation calculate_numeric_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 0.1.0 (0/1) (0/1) (1/1) (0/1) +cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) +cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) +cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) (0/1) +charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 1.0.1 r-getopt (0/1) (0/1) (0/1) (0/1) +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) (10/10) +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) (0/2) +chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm To update https://github.com/B-UMMI/chewBBACA/tree/master Variant Analysis chewbbaca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca chewbbaca 3.3.4 (0/8) (0/8) (8/8) (0/8) +chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) (0/5) +chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing To update https://github.com/cumbof/chopin2 Machine Learning chopin2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1.0.8.post1 chopin2 (1/1) (0/1) (0/1) (0/1) +chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) (1/1) +circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) +circos 21787.0 1018.0 circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy galactic_circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. Sequence visualisation To update http://circos.ca/ Graphics circos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos 0.69.8 circos 0.69.9 (11/11) (11/11) (11/11) (11/11) +cite_seq_count 18.0 1.0 cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Up-to-date https://github.com/Hoohm/CITE-seq-Count Transcriptomics cite_seq_count iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.4 (1/1) (0/1) (1/1) (0/1) +clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. Variant calling Molecular genetics To update https://github.com/HKU-BAL/Clair3 Sequence Analysis, Variant Analysis clair3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 0.1.12 clair3 1.0.7 (0/1) (0/1) (1/1) (0/1) +clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) +cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 1.0.2 cnv-phenopacket (0/1) (0/1) (1/1) (0/1) +cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 1.0.4 cnv-vcf2json (0/1) (0/1) (1/1) (0/1) +cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation To update https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.10 cnvkit 0.9.11 (0/17) (0/17) (17/17) (0/17) +codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) +colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) +collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) (1/1) +collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) (1/1) +column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.0 python (1/1) (1/1) (1/1) (1/1) +column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) (1/1) +column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by header To update Text Manipulation column_remove_by_header iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1.0 python (1/1) (1/1) (1/1) (1/1) +compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) +compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) (1/1) +compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) (0/1) +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) +coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) (0/1) +coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) +crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) (0/1) +crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) (0/1) +crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) (0/7) +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.8 cutadapt 4.8 (1/1) (1/1) (1/1) (1/1) +cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 1.0.8 cutesv 2.1.1 (0/1) (1/1) (1/1) (0/1) +cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) (0/1) +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) +das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics dastool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Read binning Metagenomics Up-to-date https://github.com/cmks/DAS_Tool Metagenomics das_tool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool 1.1.7 das_tool 1.1.7 (0/2) (0/2) (2/2) (2/2) +data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool To update Data Source data_source_iris_tcga iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 1.0.0 python (0/1) (0/1) (0/1) (0/1) +datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. To update https://www.gnu.org/software/datamash/ Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 1.8 datamash 1.1.0 (3/3) (3/3) (3/3) (3/3) +decontaminator 99.0 15.0 decontaminator Deep Learning method for novel virus detection in sequencing data decontaminator decontaminator To update https://github.com/cbib/decontaminator Machine Learning decontaminator iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +deepmicro 501.0 3.0 deepmicro Representation learning and classification framework DeepMicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. Essential dynamics, Splitting, Community profiling Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Up-to-date https://github.com/paulzierep/DeepMicro Machine Learning deepmicro iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro 1.4 deepmicro 1.4 (0/1) (0/1) (1/1) (0/1) +deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) (1/1) +deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) (0/1) +deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) (1/1) +delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) (0/6) +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) +dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) +diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) (1/1) +dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 (0/1) (0/1) (0/1) (0/1) +disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco 1.2 (1/1) (0/1) (1/1) (0/1) +dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) (0/1) +dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) (0/1) +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram 1.3.5 dram 1.5.0 (0/5) (0/5) (5/5) (0/5) +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis To update https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep 3.4.5 drep 3.5.0 (0/2) (0/2) (2/2) (2/2) +dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) (0/1) +ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) (0/2) +edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) (1/1) +egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 (1/1) (1/1) (1/1) (0/1) +emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) (107/107) +ena_upload 208.0 14.0 ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). Up-to-date https://github.com/usegalaxy-eu/ena-upload-cli Data Export ena_upload iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0.7.1 ena-upload-cli 0.7.1 (0/1) (1/1) (1/1) (1/1) +enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API To update https://github.com/bebatut/enasearch Data Source enasearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch enasearch 0.2.2 (0/5) (0/5) (5/5) (0/5) +ensembl_vep 2653.0 119.0 ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions To update https://github.com/Ensembl/ensembl-vep Variant Analysis ensembl_vep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 110.1 ensembl-vep 111.0 (0/1) (0/1) (1/1) (0/1) +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Epigenetics episcanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 (2/3) (0/3) (3/3) (0/3) +exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) (0/1) +exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) (1/1) +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. Conversion Taxonomy, Metabolomics, Biomarkers To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) (1/1) +extract_genomic_dna 11348.0 285.0 Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. To update Genomic Interval Operations extract_genomic_dna iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 3.0.3+galaxy2 bx-python 0.11.0 (1/1) (0/1) (1/1) (0/1) +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) (0/1) +fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) (0/1) +fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 2.0 numpy (1/1) (1/1) (1/1) (1/1) +fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani 1.3 fastani 1.34 (0/1) (0/1) (1/1) (1/1) +fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers Up-to-date https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp 0.23.4 fastp 0.23.4 (1/1) (1/1) (1/1) (1/1) +fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy0 fastqc 0.12.1 (1/1) (1/1) (1/1) (1/1) +fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) +fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) +feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) (1/1) +fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) (0/2) +fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) (1/1) +filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering, Sequencing quality control Up-to-date https://github.com/rrwick/Filtlong Fastq Manipulation, Sequence Analysis filtlong iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong 0.2.1 filtlong 0.2.1 (1/1) (1/1) (1/1) (1/1) +flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) (0/2) +flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) (0/1) +fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan 1.31 (0/1) (1/1) (1/1) (1/1) +freebayes 153548.0 3059.0 freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases To update https://github.com/ekg/freebayes Variant Analysis freebayes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes 1.3.6 freebayes 1.3.7 (2/2) (2/2) (2/2) (2/2) +freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining To update http://boevalab.inf.ethz.ch/FREEC/ Variant Analysis control_freec iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec 11.6 gawk (0/1) (0/1) (1/1) (0/1) +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja 1.4.4 freyja 1.5.0 (2/4) (0/4) (4/4) (0/4) +fsd fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families To update Graphics duplex_family_size_distribution iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 1.0.2 matplotlib (4/4) (0/4) (0/4) (0/4) +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Genome annotation Genomics To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) (5/5) +gatk4 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK To update https://software.broadinstitute.org/gatk/gatk4 Variant Analysis gatk4_mutect2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 4.1.7.0 gatk4 4.5.0.0 (1/1) (0/1) (1/1) (0/1) +gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format To update http://bioinf.iasi.cnr.it/gdcwebapp/ Data Source, Convert Formats gdcwebapp iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1.0.0 python (1/1) (0/1) (1/1) (0/1) +gecko 519.0 112.0 gecko Ungapped genome comparison Up-to-date https://github.com/otorreno/gecko Sequence Analysis gecko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 1.2 gecko 1.2 (0/1) (1/1) (1/1) (0/1) +gemini 1209.0 gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://github.com/arq5x/gemini Sequence Analysis, Next Gen Mappers gemini iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini 0.20.1 gemini 0.30.2 (1/3) (2/3) (2/3) (2/3) +genebed_maf_to_fasta 2.0 GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ Genomic Interval Operations genebed_maf_to_fasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1.0.1+galaxy0 (1/1) (1/1) (1/1) (1/1) +genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility To update https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html Variant Analysis genehunter_modscore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 3.0.0 ghm 3.1 (0/1) (0/1) (0/1) (0/1) +geneiobio 44.0 3.0 gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. To update https://github.com/iobio/gene.iobio Sequence Analysis geneiobio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 4.7.1+galaxy1 (0/1) (1/1) (1/1) (0/1) +genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." To update ChIP-seq genetrack iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack numpy (1/1) (0/1) (0/1) (0/1) +genomescope 2118.0 329.0 genomescope Analyze unassembled short reads Up-to-date https://github.com/tbenavi1/genomescope2.0 Statistics genomescope iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 2.0 genomescope2 2.0 (1/1) (1/1) (1/1) (1/1) +genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 (0/1) (0/1) (1/1) (0/1) +genrich 3515.0 79.0 genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). To update https://github.com/jsh58/Genrich ChIP-seq genrich iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 0.5+galaxy2 genrich 0.6.1 (1/1) (1/1) (1/1) (0/1) +get_hrun 4.0 1.0 get_hrun Annotate indel variants with homopolymer context To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun Variant Analysis get_hrun iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.1 (0/1) (0/1) (1/1) (0/1) +getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle 1.7.7.1 getorganelle 1.7.7.1 (0/2) (2/2) (2/2) (0/2) +gfa_to_fa 8274.0 332.0 gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format To update http://gfa-spec.github.io/GFA-spec/ Convert Formats gfa_to_fa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 0.1.2 (1/1) (1/1) (1/1) (1/1) +gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) (1/1) +gffcompare 3477.0 381.0 gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 (1/1) (1/1) (1/1) (1/1) +gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) (1/1) +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) (5/5) +ggupset emc-ggupset Create Upset Plots with ggupset To update https://github.com/const-ae/ggupset Graphics ggupset iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 1.0 r-ggupset (0/1) (0/1) (0/1) (0/1) +glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) (0/8) +goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) (2/2) +goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) (1/1) +gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more To update https://biit.cs.ut.ee/gprofiler Statistics, Web Services gprofiler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 (5/5) (0/5) (5/5) (0/5) +graphembed 63.0 2.0 graphembed Compute a 2D embedding of a data matrix given supervised class information Up-to-date https://github.com/fabriziocosta/GraphEmbed Statistics, Graphics graphembed iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 2.4 graph_embed 2.4 (1/1) (0/1) (1/1) (0/1) +graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics To update https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan 1.1.3 (2/2) (2/2) (2/2) (2/2) +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Up-to-date https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk 2.3.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) (0/1) +gtfToBed12 gtftobed12 Convert GTF files to BED12 format UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README Convert Formats gtftobed12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 357 ucsc-gtftogenepred 447 (1/1) (1/1) (1/1) (1/1) +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins 3.2.1 gubbins 3.3.5 (1/1) (1/1) (1/1) (0/1) +gvcftools gvcftools_extract_variants To update https://github.com/sequencing/gvcftools Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0.1 gvcftools 0.17.0 (0/1) (0/1) (0/1) (0/1) +gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) (0/1) +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) +hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) +hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) (0/1) +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) +happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) (0/1) +heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.1.3.1 r-gplots 2.17.0 (1/1) (1/1) (1/1) (1/1) +heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) (4/40) +hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.1.5 hicstuff 3.2.2 (0/1) (0/1) (0/1) (0/1) +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) +hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) (1/1) +hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 To update https://pypi.org/project/hivclustering/ Next Gen Mappers hivclustering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 1.3.1 python-hivclustering 1.6.8 (0/1) (0/1) (0/1) (0/1) +hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Up-to-date http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 3.4 hmmer 3.4 (0/12) (12/12) (12/12) (12/12) +homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) (4/5) +htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis Up-to-date https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count 2.0.5 htseq 2.0.5 (1/1) (1/1) (1/1) (1/1) +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann 3.8 humann 3.8 (6/13) (12/13) (13/13) (13/13) +hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper 2.1.6 hybpiper 2.1.6 (0/1) (1/1) (1/1) (0/1) +hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy 2.5.47 hyphy 2.5.60 (17/17) (2/17) (17/17) (2/17) +hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) (0/1) +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation To update https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen 1.3.1 icescreen 1.3.2 (0/1) (0/1) (0/1) (0/1) +idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) (3/3) +idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) (0/1) +idr_download idr_download_by_ids Image Data Resource downloading tool To update https://idr.openmicroscopy.org Data Source idr_download_by_ids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0.44.1 omero-py 5.11.1 (0/1) (0/1) (1/1) (1/1) +iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) (0/1) +instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification SNP detection, Genome comparison Mapping, Metagenomics To update https://instrain.readthedocs.io/en/latest/# Metagenomics instrain iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain 1.5.3 instrain 1.8.1 (0/2) (0/2) (2/2) (0/2) +integron_finder 52965.0 58.0 integron_finder """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Up-to-date https://github.com/gem-pasteur/Integron_Finder Sequence Analysis integronfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder 2.0.3 integron_finder 2.0.3 (0/1) (1/1) (1/1) (1/1) +intermine_galaxy_exchange 44.0 1.0 galaxy_intermine_exchange InterMine Exporter To update Convert Formats intermine_galaxy_exchange iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 0.0.1 coreutils 8.25 (1/1) (1/1) (1/1) (0/1) +interproscan 5294.0 554.0 interproscan Interproscan queries the interpro database and provides annotations. interproscan_ebi interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis To update http://www.ebi.ac.uk/Tools/pfa/iprscan5/ Sequence Analysis interproscan bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan 5.59-91.0 interproscan 5.59_91.0 (1/1) (1/1) (1/1) (1/1) +interval2maf 14.0 3.0 Interval2Maf1 Extract MAF blocks given a set of intervals bx-python bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. Sequence analysis To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations interval2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf 1.0.1+galaxy1 bx-python 0.11.0 (1/1) (1/1) (1/1) (1/1) +intervene 1497.0 136.0 intervene_pairwise, intervene_upset Create pairwise and upset plots intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Sequence comparison, Sequence visualisation Computational biology Up-to-date https://intervene.readthedocs.io Statistics intervene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene 0.6.5 intervene 0.6.5 (2/2) (0/2) (2/2) (0/2) +iqtree 21598.0 681.0 iqtree Efficient phylogenomic software by maximum likelihood iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time Phylogenetic analysis, Sequence analysis Phylogenetics To update http://www.iqtree.org/ Phylogenetics iqtree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree 2.1.2 iqtree 2.3.0 (1/1) (1/1) (1/1) (0/1) +irissv 29.0 4.0 irissv Refine insertion sequences To update https://github.com/mkirsche/Iris Variant Analysis irissv iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 1.0.4 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +isescan 57581.0 50.0 isescan """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" ISEScan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation To update https://github.com/xiezhq/ISEScan Sequence Analysis ISEScan iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan 1.7.2.3 isescan 1.7.2.1 (0/1) (1/1) (1/1) (1/1) +isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 (1/1) (1/1) (1/1) (1/1) +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) (5/5) +iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Statistics and probability To update https://bioconductor.org/packages/release/bioc/html/IWTomics.html Statistics iwtomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics 1.0.0 bioconductor-iwtomics 1.26.0 (3/3) (3/3) (3/3) (0/3) +jasminesv 30.0 3.0 jasminesv Merge structural variants across samples To update https://github.com/mkirsche/Jasmine/ Variant Analysis jasminesv iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1.0.11 jasminesv 1.1.5 (1/1) (0/1) (1/1) (0/1) +jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) (2/2) +jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) (1/1) +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) (1/1) +join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier To update Text Manipulation join_files_by_id iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 1.0 r-data.table 1.11.6 (0/1) (0/1) (0/1) (0/1) +jq 2312.0 21.0 jq JQ is a lightweight and flexible command-line JSON processor To update https://stedolan.github.io/jq/ Text Manipulation jq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1.0 jq 1.5 (1/1) (1/1) (1/1) (1/1) +jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics Up-to-date https://lindenb.github.io/jvarkit/ SAM jvarkit iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 20201223 jvarkit-wgscoverageplotter 20201223 (1/1) (0/1) (1/1) (0/1) +kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.50.1 (2/2) (2/2) (2/2) (2/2) +kc-align kc-align Kc-Align custom tool kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) (0/1) +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) (0/8) +king 5.0 3.0 king Kinship-based INference for Gwas Up-to-date http://people.virginia.edu/~wc9c/KING/ Variant Analysis king iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 2.2.7 king 2.2.7 (0/1) (0/1) (1/1) (0/1) +kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) (0/1) +kma kma_map Map with KMA To update https://bitbucket.org/genomicepidemiology/kma Next Gen Mappers kma iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 1.2.21 kma 1.4.14 (0/1) (0/1) (1/1) (0/1) +kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Sequence analysis, Gene functional annotation Genomics Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) (1/1) +kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) (1/1) +kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report Kraken-Taxonomy-Report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples Visualisation, Classification Metagenomics, Taxonomy To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (1/1) (1/1) (0/1) +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools 1.2 krakentools 1.2 (1/6) (6/6) (6/6) (6/6) +krocus krocus Predict MLST directly from uncorrected long reads krocus krocus krocus Predict MLST directly from uncorrected long reads Multilocus sequence typing, k-mer counting Public health and epidemiology To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (1/1) (0/1) +last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last 1205 last 1542 (0/5) (0/5) (5/5) (5/5) +lastz 83331.0 188.0 lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. Sequence alignment, Read mapping Genomics Up-to-date https://github.com/lastz/lastz Next Gen Mappers lastz devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz 1.04.22 lastz 1.04.22 (2/2) (2/2) (2/2) (2/2) +lcrgenie lcrgenie Ligase Chain Reaction Genie To update https://github.com/neilswainston/LCRGenie Synthetic Biology lcrgenie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 1.0.2 lcr_genie (0/1) (0/1) (0/1) (0/1) +legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing Sequence analysis Public health and epidemiology Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) (0/1) +length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) (1/1) +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) (1/1) +lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot 1.6.0 r-base (0/1) (0/1) (1/1) (0/1) +links 405.0 77.0 links Scaffold genome assemblies with long reads. links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) (0/1) +lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. Up-to-date https://csb5.github.io/lofreq/ Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 2.1.5 lofreq 2.1.5 (5/5) (5/5) (5/5) (4/5) +lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Sequence analysis, Genotyping Genotype and phenotype Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) (0/1) +lumpy_sv 358.0 50.0 lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery Up-to-date http://layerlab.org/software/ Variant Analysis lumpy_sv iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0.3.1 lumpy-sv 0.3.1 (0/2) (0/2) (2/2) (0/2) +m6anet 3.0 m6anet m6anet to detect m6A RNA modifications from nanopore data m6Anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning Up-to-date https://m6anet.readthedocs.io/en/latest Sequence Analysis m6anet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet 2.1.0 m6anet 2.1.0 (0/1) (0/1) (1/1) (0/1) +maaslin2 188.0 29.0 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability To update http://huttenhower.sph.harvard.edu/maaslin Metagenomics maaslin2 iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 0.99.12 maaslin2 1.16.0 (0/1) (0/1) (1/1) (0/1) +macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq macs macs MACS Model-based Analysis of ChIP-seq data. Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites Up-to-date https://github.com/taoliu/MACS Sequence Analysis, Statistics macs2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 2.2.9.1 macs2 2.2.9.1 (9/9) (9/9) (9/9) (9/9) +maf_stats 8.0 2.0 maf_stats1 MAF Coverage statistics To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ Genomic Interval Operations maf_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1.0.2+galaxy0 (1/1) (1/1) (1/1) (1/1) +mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Genetic variation analysis Genetics, Genetic variation, Genomics To update https://sourceforge.net/projects/mageck/ Genome editing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck 0.5.9.2 mageck 0.5.9.5 (3/5) (5/5) (5/5) (0/5) +maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) +malt malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. To update https://github.com/husonlab/malt Next Gen Mappers malt_run iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0.5.3 malt 0.62 (0/1) (0/1) (1/1) (0/1) +map_param_value 1528.0 9.0 map_param_value Map a parameter value to another value To update Text Manipulation map_param_value iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 0.2.0 (1/1) (0/1) (1/1) (0/1) +mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) +mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) +mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) +masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) (0/1) +maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) +mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) +medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) (3/4) +megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) +megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (0/1) +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) (0/4) +meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) (0/1) +meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) +merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) (0/1) +merqury 2483.0 244.0 merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury 1.3 merqury 1.3 (2/2) (2/2) (2/2) (2/2) +meryl 6785.0 350.0 meryl Meryl a k-mer counter. meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) (1/1) +metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. MetaBAT_2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Up-to-date https://bitbucket.org/berkeleylab/metabat/src/master/ Metagenomics metabat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 2.15 metabat2 2.15 (2/2) (1/2) (2/2) (2/2) +metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) +metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) +metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.0 (1/4) (2/4) (4/4) (4/4) +metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (0/1) (0/1) +migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) +minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) +miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) +minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 (1/1) (1/1) (1/1) (1/1) +miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) +mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) +mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) +mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) (0/1) +mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.6 mitos 2.1.8 (1/2) (1/2) (2/2) (0/2) +mlst 9304.0 635.0 mlst, mlst_list Scan contig files against PubMLST typing schemes mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. Multilocus sequence typing Immunoproteins and antigens To update https://github.com/tseemann/mlst Sequence Analysis mlst iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst 2.22.0 mlst 2.23.0 (2/2) (2/2) (2/2) (2/2) +moabs 317.0 19.0 moabs MOABS for differential methylation analysis on Bisulfite sequencing data. To update https://github.com/sunnyisgalaxy/moabs Epigenetics moabs iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 1.3.4.6 moabs 1.3.9.0 (0/1) (0/1) (1/1) (0/1) +mosdepth 262.0 21.0 mosdepth fast and flexible BAM/CRAM depth calculation Up-to-date https://github.com/brentp/mosdepth SAM mosdepth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 0.3.7 mosdepth 0.3.7 (0/1) (0/1) (1/1) (0/1) +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn Mothur wrappers mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny To update https://www.mothur.org Metagenomics mothur iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur 1.0 mothur 1.48.0 (129/129) (129/129) (129/129) (129/129) +msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) (0/1) +multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) (0/1) +multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.21 (1/1) (1/1) (1/1) (1/1) +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) (6/6) +mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) +mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) (0/1) +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) Up-to-date https://github.com/BlankenbergLab/nAltORFs Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 0.1.2 naltorfs 0.1.2 (3/3) (0/3) (0/3) (0/3) +nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) +nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) +ncbi_acc_download 5487.0 688.0 ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API Up-to-date https://github.com/kblin/ncbi-acc-download Data Source ncbi_acc_download iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 0.2.8 ncbi-acc-download 0.2.8 (1/1) (1/1) (1/1) (1/1) +ncbi_datasets 3177.0 667.0 datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. Data handling, Sequence database search, Data retrieval Biological databases To update https://github.com/ncbi/datasets Data Source ncbi_datasets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets 16.6.0 ncbi-datasets-cli (2/2) (0/2) (2/2) (2/2) +ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases To update http://www.ncbi.nlm.nih.gov/books/NBK179288/ Data Source ncbi_entrez_direct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 16.2 entrez-direct 21.6 (0/3) (0/3) (0/3) (0/3) +ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases To update https://www.ncbi.nlm.nih.gov/books/NBK25501/ Data Source ncbi_entrez_eutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 1.70 python (0/8) (0/8) (8/8) (0/8) +ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) +necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) (0/1) +newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) +nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) +ngmlr 1266.0 21.0 ngmlr CoNvex Gap-cost alignMents for Long Reads ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Up-to-date https://github.com/philres/ngmlr Next Gen Mappers ngmlr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr 0.2.7 ngmlr 0.2.7 (0/1) (0/1) (1/1) (0/1) +ngsutils ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics To update https://github.com/ngsutils/ngsutils SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils 0.5.9 (1/1) (1/1) (1/1) (1/1) +nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity Operation To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) (1/1) +novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 4.3.1 novoplasty 4.3.5 (0/1) (1/1) (1/1) (1/1) +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) +obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) +ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1) (0/1) +odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.8.6 (0/2) (0/2) (2/2) (2/2) +omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4) (0/4) +onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18) (0/18) +optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1) (0/1) +optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) (0/1) +orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) +orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) +packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) (0/1) +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.0.3 pairtools 1.0.3 (0/5) (0/5) (5/5) (0/5) +pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) +parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) +pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) +pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference genomicconsensus genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. Variant calling Mapping Up-to-date https://github.com/PacificBiosciences/gcpp Variant Analysis pbgcpp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp 2.0.2 pbgcpp 2.0.2 (0/1) (0/1) (0/1) (0/1) +pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Pairwise sequence alignment, Sorting Mapping Up-to-date https://github.com/PacificBiosciences/pbmm2 Next Gen Mappers pbmm2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 1.13.1 pbmm2 1.13.1 (0/1) (0/1) (1/1) (0/1) +pbtk bam2fastx Convert PacBio Bam File to fasta or fastq file Up-to-date https://github.com/PacificBiosciences/pbtk Convert Formats, Fasta Manipulation, Fastq Manipulation bam2fastx iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 3.1.1 pbtk 3.1.1 (1/1) (0/1) (1/1) (0/1) +pe_histogram 4180.0 312.0 pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram Graphics pe_histogram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1.0.1 openjdk (1/1) (1/1) (1/1) (1/1) +peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. To update https://github.com/steinmann/peakzilla ChIP-seq peakzilla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 1.0 python (0/1) (0/1) (1/1) (0/1) +pear 4305.0 150.0 iuc_pear PEAR evaluates all possible paired-end read overlaps pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Sequence merging Sequence assembly Up-to-date pear iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear 0.9.6 pear 0.9.6 (1/1) (1/1) (1/1) (0/1) +pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " + pharokka + " (0/1) (1/1) (1/1) (0/1) +phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) +phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) +picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_reordersam, picard_samtofastq, picard_fastqtosam, picard_replacesamheader picard_samtofastq Create a FASTQ file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31) (31/31) +pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (1/1) (1/1) (0/1) +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) +pilon 7942.0 467.0 pilon pilon is a tool for assembly improvement and variant analysis in bacteria pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. Sequence assembly, Analysis, Read alignment Assembly To update Variant Analysis pilon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon 1.20.1 pilon 1.24 (1/1) (1/1) (1/1) (1/1) +pipelign 983.0 83.0 pipelign Multipe sequence alignment Up-to-date https://github.com/asmmhossain/pipelign/ Next Gen Mappers pipelign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 0.2 pipelign 0.2 (1/1) (0/1) (1/1) (0/1) +pizzly 208.0 16.0 pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 (1/1) (0/1) (1/1) (0/1) +plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) +plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) +plink 669.0 46.0 plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Genetic variation analysis GWAS study Up-to-date https://www.cog-genomics.org/plink Genome-Wide Association Study plink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink 1.90b6.21 plink 1.90b6.21 (1/1) (0/1) (1/1) (1/1) +polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) +porechop 185468.0 1046.0 porechop Porechop - Finding and removing adapters from Oxford Nanopore reads To update https://github.com/rrwick/Porechop Fasta Manipulation, Fastq Manipulation porechop iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop porechop 0.2.4 (1/1) (1/1) (1/1) (0/1) +poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Nucleic acid sequence analysis DNA, Sequencing Up-to-date https://poretools.readthedocs.io/en/latest/ Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools 0.6.1a1 poretools 0.6.1a1 (13/13) (13/13) (13/13) (0/13) +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) (0/11) +pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 (3/3) (2/3) (3/3) (0/3) +prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) (1/1) +prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) +progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) (0/2) +prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) +prot-scriber prot_scriber Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.4 prot-scriber 0.1.5 (0/1) (0/1) (1/1) (0/1) +proteinortho 2092.0 125.0 proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species Sequence clustering, Sequence analysis Comparative genomics Up-to-date https://gitlab.com/paulklemm_PHD/proteinortho Proteomics proteinortho iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho 6.3.1 proteinortho 6.3.1 (0/3) (0/3) (3/3) (0/3) +psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 (0/1) (0/1) (1/1) (0/1) +pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) (0/1) +purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) (0/1) +pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) +pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 (1/1) (0/1) (1/1) (0/1) +pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.8 (1/1) (1/1) (1/1) (1/1) +pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) (0/1) +qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) (0/1) +qiime_add_on qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime 1.9.1 (0/2) (0/2) (2/2) (2/2) +qiime_core qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file QIIME to perform microbial community analysis To update http://www.qiime.org Metagenomics qiime iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime 1.9.1 (0/32) (0/32) (32/32) (32/32) +qq_tools qq_manhattan To update https://CRAN.R-project.org/package=qqman Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0.1.0 r-qqman 0.1.4 (0/1) (0/1) (0/1) (0/1) +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Sequencing quality control Data quality management To update http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.2.2d qualimap 2.3 (4/4) (4/4) (4/4) (1/4) +quast 51567.0 3567.0 quast Quast (Quality ASsessment Tool) evaluates genome assemblies. quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. Visualisation, Sequence assembly validation Sequence assembly Up-to-date http://quast.bioinf.spbau.ru/ Assembly quast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast 5.2.0 quast 5.2.0 (1/1) (1/1) (1/1) (1/1) +query_impc 1.0 query_impc Contains a tool to query the IMPC database. To update https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc Convert Formats, Web Services query_impc iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0.9.0 requests (0/1) (0/1) (1/1) (0/1) +query_tabular 20860.0 168.0 filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3.3.0 python (3/3) (3/3) (3/3) (1/3) +quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Up-to-date https://github.com/mahulchak/quickmerge Assembly quickmerge galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge 0.3 quickmerge 0.3 (0/1) (0/1) (0/1) (0/1) +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 (5/5) (5/5) (5/5) (1/5) +ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1) (1/1) +rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1) (1/1) +rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa rasusa Produces an unbiased subsample of your reads Up-to-date https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa 0.8.0 rasusa 0.8.0 (0/1) (0/1) (1/1) (0/1) +raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) (1/1) +raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) (1/1) +rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 (0/1) (0/1) (1/1) (0/1) +read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads read_it_and_keep read_it_and_keep read_it_and_keep Read contamination removal Filtering, Genome alignment Pathology, Genomics To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) (0/1) +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge 1.14.0 recentrifuge 1.14.0 (0/1) (0/1) (1/1) (1/1) +red 578.0 88.0 red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) (1/1) +repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) (1/1) +repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) (1/1) +repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. To update ChIP-seq repmatch_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 matplotlib (1/1) (0/1) (0/1) (0/1) +reshape2 cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast To update https://cran.r-project.org/web/packages/reshape2/index.html Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 1.4.2 r-reshape2 (2/2) (0/2) (2/2) (2/2) +resize_coordinate_window 85.0 5.0 resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. To update Genomic Interval Operations resize_coordinate_window iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1.0.2 python (1/1) (0/1) (1/1) (0/1) +revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) +rgcca 44.0 3.0 rgcca multi-block analysis To update https://github.com/rgcca-factory/RGCCA Statistics rgcca iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 3.0.2 rgccacmd 3.0.3 (1/1) (0/1) (1/1) (0/1) +rgrnastar 416677.0 3843.0 rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b (2/2) (2/2) (2/2) (1/2) +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) (0/2) +rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.2.3 rnaquast 2.2.3 (1/1) (0/1) (1/1) (1/1) +roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) +rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output To update https://github.com/brsynth/rp2biosensor Synthetic Biology rp2biosensor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 3.2.1 rp2biosensor (0/1) (0/1) (0/1) (0/1) +rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 To update https://github.com/brsynth/rp2paths Synthetic Biology rp2paths iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 1.5.1 rp2paths (0/1) (0/1) (0/1) (0/1) +rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files To update https://github.com/brsynth/rpbasicdesign Synthetic Biology rpbasicdesign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 1.2.2 rpbasicdesign (0/1) (0/1) (0/1) (0/1) +rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways To update https://github.com/brsynth/rptools/releases Synthetic Biology rpfba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 5.12.3 rptools (0/1) (0/1) (0/1) (0/1) +rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format To update https://github.com/brsynth/rptools Synthetic Biology rptools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 5.13.1 rptools (0/5) (0/5) (0/5) (0/5) +rrparser rrparser Reaction Rules Parser To update https://github.com/brsynth/RRParser Synthetic Biology rrparser iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 2.5.2 rrparser (0/1) (0/1) (0/1) (0/1) +rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Data handling Sequencing Up-to-date https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.3 (22/22) (22/22) (22/22) (22/22) +ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) (0/1) +salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) (0/1) +samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) (0/1) +sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.1 sansa 0.2.1 (0/1) (0/1) (1/1) (0/1) +sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) +sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) +sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol (0/1) (0/1) (0/1) (0/1) +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis scanpy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.9.6 scanpy 1.7.2 (6/6) (6/6) (6/6) (0/6) +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Transcriptomics, RNA, Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 (0/5) (5/5) (5/5) (0/5) +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Transcriptomics sceasy_convert iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 (1/1) (0/1) (1/1) (0/1) +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization schicexplorer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 (0/16) (0/16) (16/16) (0/16) +scikit-bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics Up-to-date http://scikit-bio.org/ Sequence Analysis scikit_bio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 0.4.2 scikit-bio 0.4.2 (1/1) (0/1) (0/1) (0/1) +scoary 676.0 61.0 scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Up-to-date https://github.com/AdmiralenOla/Scoary Metagenomics scoary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary 1.6.16 scoary 1.6.16 (0/1) (0/1) (1/1) (0/1) +scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, RNA, Statistics scpipe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 (1/1) (0/1) (1/1) (0/1) +seacr 3693.0 50.0 seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. Up-to-date https://github.com/FredHutch/SEACR Epigenetics, ChIP-seq seacr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1.3 seacr 1.3 (1/1) (0/1) (1/1) (0/1) +selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. Up-to-date https://github.com/brsynth/selenzy-wrapper Synthetic Biology selenzy_wrapper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0.3.0 selenzy_wrapper 0.3.0 (0/1) (0/1) (0/1) (0/1) +semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly To update https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin 2.0.2 semibin 2.1.0 (0/6) (0/6) (6/6) (1/6) +seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) (0/1) +seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) (0/1) +seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.3.1 seqkit 2.8.1 (0/5) (2/5) (3/5) (2/5) +seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.3.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) +seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) (15/15) +seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.10 (0/1) (0/1) (1/1) (0/1) +seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) +shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) (0/1) +shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) +shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) +sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) (1/1) +simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. To update https://github.com/dlal-group/simtext Text Manipulation simtext iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0.0.2 r-argparse 1.0.1 (0/4) (2/4) (4/4) (0/4) +sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) (0/1) +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools To update https://github.com/timoast/sinto Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.9.0 sinto 0.10.0 (2/2) (0/2) (2/2) (0/2) +slamdunk 361.0 2.0 alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 (2/2) (0/2) (2/2) (0/2) +sleuth 64.0 8.0 sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 (0/1) (0/1) (1/1) (0/1) +smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. v-pipe v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Up-to-date https://github.com/cbg-ethz/smallgenomeutilities Sequence Analysis smallgenomeutilities iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities 0.4.0 smallgenomeutilities 0.4.0 (0/1) (0/1) (1/1) (0/1) +smudgeplot 203.0 22.0 smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing smudgeplots smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Up-to-date https://github.com/KamilSJaron/smudgeplot Assembly smudgeplot galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot 0.2.5 smudgeplot 0.2.5 (1/1) (1/1) (1/1) (0/1) +snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. Gene prediction DNA, DNA polymorphism, Genetics Up-to-date https://github.com/KorfLab/SNAP Sequence Analysis snap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap 2013_11_29 snap 2013_11_29 (1/2) (1/2) (1/2) (0/2) +sniffles 919.0 58.0 sniffles Galaxy wrapper for sniffles sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. Sequence analysis, Structural variation detection DNA structural variation, Sequencing To update https://github.com/fritzsedlazeck/Sniffles Sequence Analysis sniffles iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles 1.0.12 sniffles 2.3.2 (1/1) (1/1) (1/1) (1/1) +snipit 669.0 22.0 snipit Summarise snps relative to a reference sequence snipit snipit snipit Summarise snps relative to a reference sequence Base position variability plotting Virology Up-to-date https://github.com/aineniamh/snipit Variant Analysis, Sequence Analysis snipit iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit 1.2 snipit 1.2 (0/1) (0/1) (1/1) (0/1) +snippy 105708.0 1372.0 snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics To update https://github.com/tseemann/snippy Sequence Analysis snippy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy 4.6.0 (3/3) (3/3) (3/3) (3/3) +snp-dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment Up-to-date https://github.com/tseemann/snp-dists Variant Analysis snp_dists iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 0.8.2 snp-dists 0.8.2 (1/1) (1/1) (1/1) (0/1) +snp-sites snp_sites Finds SNP sites from a multi-FASTA alignment file Up-to-date https://github.com/sanger-pathogens/snp-sites Variant Analysis snp_sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 2.5.1 snp-sites 2.5.1 (1/1) (1/1) (1/1) (0/1) +snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox snpeff snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff_sars_cov_2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 (1/1) (1/1) (1/1) (1/1) +snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base (1/1) (1/1) (1/1) (1/1) +socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) (0/1) +sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades rnaviralspades, biosyntheticspades, spades, metaspades, rnaspades, coronaspades, plasmidspades, metaviralspades, metaplasmidspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) +spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python (2/2) (0/2) (2/2) (0/2) +spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) +spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) +sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.0 sra-tools 3.1.0 (3/3) (3/3) (3/3) (3/3) +srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) (12/13) +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) (12/12) +star_fusion 1212.0 35.0 star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update Sequence Analysis, Transcriptomics star_fusion iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 (1/1) (1/1) (1/1) (0/1) +straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model To update https://github.com/brsynth/straindesign Systems Biology, Synthetic Biology straindesign iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 3.2.2 straindesign 3.2.3 (0/3) (0/3) (0/3) (0/3) +strelka strelka_germline, strelka_somatic Up-to-date https://github.com/Illumina/strelka/ Variant Analysis strelka iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2.9.10 strelka 2.9.10 (2/2) (0/2) (2/2) (0/2) +stringtie 167659.0 2165.0 stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq To update http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.1 stringtie 2.2.2 (2/2) (2/2) (2/2) (2/2) +structure 2623.0 59.0 structure for using multi-locus genotype data to investigate population structure. structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Genetic variation analysis Population genetics Up-to-date Phylogenetics, Variant Analysis structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure 2.3.4 structure 2.3.4 (0/1) (0/1) (1/1) (1/1) +structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method Up-to-date Phylogenetics, Variant Analysis structureharvester iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0.6.94 structureharvester 0.6.94 (0/1) (0/1) (0/1) (0/1) +swift swiftlink Parallel MCMC Linkage Analysis Up-to-date https://github.com/ajm/swiftlink Variant Analysis swiftlink iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 1.0 swiftlink 1.0 (0/1) (0/1) (0/1) (0/1) +syndiva 30.0 2.0 syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. To update Proteomics syndiva iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 1.0 clustalo 1.2.4 (0/1) (0/1) (1/1) (0/1) +table_compute 208652.0 741.0 table_compute Perform general-purpose table operations To update Text Manipulation table_compute iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1.2.4 pandas (1/1) (1/1) (1/1) (1/1) +tag_pileup_frequency 164.0 7.0 tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup Statistics, SAM, Genomic Interval Operations tag_pileup_frequency iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1.0.2 openjdk (1/1) (0/1) (1/1) (0/1) +tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches Up-to-date Sequence Analysis tasmanian_mismatch iuc https://github.com/nebiolabs/tasmanian-mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1.0.7 tasmanian-mismatch 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy To update https://github.com/pvanheus/ncbitaxonomy Sequence Analysis, Genome annotation taxonomy_filter_refseq iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0.3.0 rust-ncbitaxonomy 1.0.7 (0/1) (0/1) (0/1) (0/1) +taxonomy_krona_chart 27426.0 1801.0 taxonomy_krona_chart Krona pie chart from taxonomic profile krona krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). Visualisation Metagenomics To update http://sourceforge.net/projects/krona/ Assembly taxonomy_krona_chart crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart 2.7.1+galaxy0 krona 2.8.1 (1/1) (1/1) (1/1) (1/1) +tb-profiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). Antimicrobial resistance prediction To update https://github.com/jodyphelan/TBProfiler Sequence Analysis tbprofiler iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler 4.4.1 tb-profiler 6.2.0 (1/1) (1/1) (1/1) (0/1) +tb_variant_filter 19252.0 209.0 tb_variant_filter M. tuberculosis H37Rv VCF filter Up-to-date https://github.com/COMBAT-TB/tb_variant_filter Variant Analysis tb_variant_filter iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 (1/1) (1/1) (1/1) (0/1) +tbl2gff3 1584.0 229.0 tbl2gff3 Table to GFF3 To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 Convert Formats, Sequence Analysis tbl2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1.2 bcbiogff 0.6.6 (0/1) (1/1) (1/1) (1/1) +tbvcfreport 2290.0 167.0 tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) Up-to-date https://github.com/COMBAT-TB/tbvcfreport Variant Analysis tbvcfreport iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 0.1.10 tbvcfreport 0.1.10 (1/1) (1/1) (1/1) (0/1) +te_finder 81.0 7.0 te_finder Transposable element insertions finder tefinder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation To update https://github.com/VistaSohrab/TEfinder Sequence Analysis te_finder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder 1.0.1 samtools 1.20 (0/1) (0/1) (1/1) (0/1) +telescope telescope_assign Single locus resolution of Transposable ELEment expression. Telescope-expression Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly Up-to-date https://github.com/mlbendall/telescope/ Genome annotation telescope_assign iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope 1.0.3 telescope 1.0.3 (0/1) (0/1) (0/1) (0/1) +tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) (0/1) +tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) (0/1) +tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) (0/4) +tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.3 tracegroomer 0.1.3 (0/1) (0/1) (1/1) (1/1) +tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) (0/4) +transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) (1/1) +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) +transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) +trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) (1/1) +trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) +trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) +tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.4 (0/1) (0/1) (1/1) (1/1) +tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) (1/1) +tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) (0/1) +ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 377 ucsc-blat 445 (0/1) (0/1) (0/1) (0/1) +fasplit fasplit faSplit is a tool to split a single FASTA file into several files UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Fasta Manipulation ucsc_fasplit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit 377 ucsc-fasplit 377 (1/1) (1/1) (1/1) (1/1) +fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date http://hgdownload.cse.ucsc.edu/admin/exe/ Convert Formats ucsc_fatovcf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf 448 ucsc-fatovcf 448 (1/1) (1/1) (1/1) (0/1) +twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis To update https://genome.ucsc.edu/goldenpath/help/twoBit.html Convert Formats ucsc_twobittofa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa 377 ucsc-twobittofa 455 (1/1) (1/1) (1/1) (0/1) +wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig UCSC_Genome_Browser_Utilities UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. Sequence analysis Up-to-date https://genome.ucsc.edu/goldenPath/help/bigWig.html Convert Formats ucsc_wigtobigwig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig 447 ucsc-wigtobigwig 447 (1/1) (1/1) (1/1) (0/1) +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.2 umi_tools 1.1.5 (5/5) (5/5) (5/5) (5/5) +unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) (1/1) +usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) (0/2) +valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet 1.0 (1/1) (0/1) (1/1) (1/1) +vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) (0/1) +vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) (0/1) +variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) (0/3) +varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (3/3) (3/3) (3/3) +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.1.2 varvamp 1.1.2 (0/1) (0/1) (1/1) (0/1) +vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF Up-to-date Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.21 (0/1) (1/1) (1/1) (0/1) +vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 (0/1) (0/1) (1/1) (0/1) +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3) +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics velocyto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 (1/1) (0/1) (1/1) (0/1) +velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) (2/2) +velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) +verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.0 (0/1) (0/1) (1/1) (0/1) +vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.56.0 (0/3) (0/3) (3/3) (3/3) +virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) +virhunter 234.0 40.0 virhunter Deep Learning method for novel virus detection in sequencing data virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). Sequence classification Virology To update https://github.com/cbib/virhunter Machine Learning virhunter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter 1.0.0 numpy (0/1) (0/1) (1/1) (0/1) +volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) (1/1) +vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.27.1 (8/8) (8/8) (8/8) (8/8) +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.0 (0/5) (0/5) (0/5) (0/5) +weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) (0/1) +weblogo3 2370.0 74.0 rgweblogo3 Sequence Logo generator for fasta weblogo weblogo WebLogo Web-based application designed to make generate sequence logos. Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis To update Graphics weblogo3 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 3.5.0 weblogo 3.7.9 (1/1) (1/1) (1/1) (1/1) +windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) +winnowmap 248.0 27.0 winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. Up-to-date https://github.com/marbl/Winnowmap Next Gen Mappers winnowmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 2.03 winnowmap 2.03 (0/1) (0/1) (1/1) (0/1) +xpath 234.0 3.0 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) (0/1) +yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) (0/1) +zerone 90.0 2.0 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) (0/1) +bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) +bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) (1/1) +bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (2/4) (4/4) (0/4) +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) +cuffcompare 1130.0 65.0 cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffdiff 5831.0 228.0 cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 (1/1) (0/1) (1/1) (0/1) +cufflinks 32218.0 319.0 cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffmerge 3292.0 122.0 cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (1/1) +cuffnorm 660.0 27.0 cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +cuffquant 688.0 18.0 cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 (1/1) (1/1) (1/1) (0/1) +fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Graphics, Statistics fasta_clipping_histogram devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0.0.14 fastx_toolkit 0.0.14 (0/1) (1/1) (0/1) (0/1) +fasta_formatter 2912.0 68.0 cshl_fasta_formatter FASTA Width formatter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_formatter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fasta_nucleotide_changer 774.0 29.0 cshl_fasta_nucleotides_changer RNA/DNA converter. Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fasta_nucleotide_changer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_boxplot 1175.0 51.0 cshl_fastq_quality_boxplot Draw quality score boxplot Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics, Statistics fastq_quality_boxplot devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_converter 220.0 11.0 cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_converter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_quality_filter 15153.0 1509.0 cshl_fastq_quality_filter Filter by quality Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation fastq_quality_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_to_fasta 13599.0 419.0 cshl_fastq_to_fasta FASTQ to FASTA converter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Convert Formats fastq_to_fasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_artifacts_filter 1809.0 27.0 cshl_fastx_artifacts_filter Remove sequencing artifacts Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_artifacts_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_barcode_splitter 16589.0 128.0 cshl_fastx_barcode_splitter Barcode Splitter Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_barcode_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_clipper 3321.0 96.0 cshl_fastx_clipper Clip adapter sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_clipper devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_collapser 61218.0 114.0 cshl_fastx_collapser Collapse sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation fastx_collapser devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_nucleotides_distribution 249.0 25.0 cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Graphics fastx_nucleotides_distribution devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_quality_statistics 2162.0 63.0 cshl_fastx_quality_statistics Compute quality statistics Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Statistics fastx_quality_statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_renamer 2280.0 68.0 cshl_fastx_renamer Rename sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_renamer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_reverse_complement 10831.0 156.0 cshl_fastx_reverse_complement Reverse-Complement Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fastq Manipulation, Fasta Manipulation fastx_reverse_complement devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastx_trimmer 13148.0 205.0 cshl_fastx_trimmer Trim sequences Up-to-date http://hannonlab.cshl.edu/fastx_toolkit/ Fasta Manipulation, Fastq Manipulation fastx_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 0.0.14 fastx_toolkit 0.0.14 (1/1) (1/1) (1/1) (1/1) +fastq_combiner 8676.0 66.0 fastq_combiner Combine FASTA and QUAL into FASTQ Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation, Fasta Manipulation fastq_combiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_filter 14222.0 266.0 fastq_filter Filter FASTQ reads by quality score and length Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_filter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_groomer 94802.0 1028.0 fastq_groomer Convert between various FASTQ quality formats. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_groomer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_manipulation 2503.0 69.0 fastq_manipulation Manipulate FASTQ reads on various attributes. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_masker_by_quality 170.0 16.0 fastq_masker_by_quality FASTQ Masker by quality score Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_masker_by_quality devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_deinterlacer 8410.0 122.0 fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_deinterlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_interlacer 17024.0 1087.0 fastq_paired_end_interlacer FASTQ interlacer on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_interlacer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_joiner 16635.0 245.0 fastq_paired_end_joiner FASTQ joiner on paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_joiner devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_paired_end_splitter 3092.0 196.0 fastq_paired_end_splitter FASTQ splitter on joined paired end reads Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_paired_end_splitter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_stats 4246.0 221.0 fastq_stats FASTQ Summary Statistics by column Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_stats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_to_tabular 12593.0 93.0 fastq_to_tabular FASTQ to Tabular converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_to_tabular devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastq_trimmer 9757.0 210.0 fastq_trimmer FASTQ Trimmer by quality Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastq_trimmer devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +fastqtofasta 178172.0 1371.0 fastq_to_fasta_python FASTQ to FASTA converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation fastqtofasta devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (0/1) +tabular_to_fastq 7388.0 200.0 tabular_to_fastq Tabular to FASTQ converter Up-to-date https://github.com/galaxyproject/sequence_utils Fastq Manipulation tabular_to_fastq devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1.1.5 galaxy_sequence_utils 1.1.5 (1/1) (1/1) (1/1) (1/1) +kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) +samtools To update https://github.com/samtools/samtools SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 1.15.1 samtools 1.20 (0/1) (0/1) (0/1) (0/1) +snpeff 101254.0 2843.0 snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox To update http://snpeff.sourceforge.net/ Genome-Wide Association Study, Variant Analysis snpeff iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff biopython 1.70 (5/5) (5/5) (5/5) (5/5) +snpsift 5109063.0 1185.0 snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html Variant Analysis snpsift iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift snpsift 5.2 (8/8) (8/8) (8/8) (8/8) +snpsift_dbnsfp 46.0 11.0 snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani To update http://snpeff.sourceforge.net/SnpSift.html#dbNSFP Variant Analysis snpsift_dbnsfp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +snpsift_genesets 390.0 11.0 snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome To update http://snpeff.sourceforge.net/SnpSift.html#geneSets Variant Analysis snpsift_genesets iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets snpsift 5.2 (1/1) (0/1) (1/1) (0/1) +vcf2tsv 167913.0 352.0 vcf2tsv Converts VCF files into tab-delimited format To update https://github.com/ekg/vcflib Variant Analysis, Convert Formats vcf2tsv devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfaddinfo 357.0 8.0 vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfaddinfo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfallelicprimitives 15803.0 286.0 vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines To update https://github.com/ekg/vcflib Variant Analysis vcfallelicprimitives devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfannotate 2181.0 77.0 vcfannotate Intersect VCF records with BED annotations To update https://github.com/ekg/vcflib Variant Analysis vcfannotate devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfannotategenotypes 192.0 28.0 vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. To update https://github.com/ekg/vcflib Variant Analysis vcfannotategenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbedintersect 3217.0 80.0 vcfbedintersect Intersect VCF and BED datasets To update https://github.com/ekg/vcflib Variant Analysis vcfbedintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfbreakcreatemulti 471.0 13.0 vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record To update https://github.com/ekg/vcflib Variant Analysis vcfbreakcreatemulti devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcheck 675.0 39.0 vcfcheck Verify that the reference allele matches the reference genome To update https://github.com/ekg/vcflib Variant Analysis vcfcheck devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcombine 1695.0 99.0 vcfcombine Combine multiple VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfcombine devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfcommonsamples 244.0 14.0 vcfcommonsamples Output records belonging to samples commong between two datasets. To update https://github.com/ekg/vcflib Variant Analysis vcfcommonsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfdistance 564.0 40.0 vcfdistance Calculate distance to the nearest variant. To update https://github.com/ekg/vcflib Variant Analysis vcfdistance devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffilter 44444.0 882.0 vcffilter2 Tool for filtering VCF files To update https://github.com/ekg/vcflib Variant Analysis vcffilter devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcffixup 917.0 71.0 vcffixup Count the allele frequencies across alleles present in each record in the VCF file. To update https://github.com/ekg/vcflib Variant Analysis vcffixup devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfflatten 177.0 6.0 vcfflatten2 Removes multi-allelic sites by picking the most common alternate To update https://github.com/ekg/vcflib Variant Analysis vcfflatten devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgeno2haplo 718.0 36.0 vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles To update https://github.com/ekg/vcflib Variant Analysis vcfgeno2haplo devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfgenotypes 451.0 48.0 vcfgenotypes Convert numerical representation of genotypes to allelic. To update https://github.com/ekg/vcflib Variant Analysis vcfgenotypes devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfhethom 1370.0 90.0 vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. To update https://github.com/ekg/vcflib Variant Analysis vcfhethom devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfleftalign 279.0 10.0 vcfleftalign Left-align indels and complex variants in VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfleftalign devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfprimers 708.0 12.0 vcfprimers Extract flanking sequences for each VCF record To update https://github.com/ekg/vcflib Variant Analysis vcfprimers devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfrandomsample 159.0 5.0 vcfrandomsample Randomly sample sites from VCF dataset To update https://github.com/ekg/vcflib Variant Analysis vcfrandomsample devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfselectsamples 854.0 29.0 vcfselectsamples Select samples from a VCF file To update https://github.com/ekg/vcflib Variant Analysis vcfselectsamples devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfsort 1852.0 63.0 vcfsort Sort VCF dataset by coordinate To update https://github.com/ekg/vcflib Variant Analysis vcfsort devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) +vcfvcfintersect 972774.0 265.0 vcfvcfintersect Intersect two VCF datasets To update https://github.com/ekg/vcflib Variant Analysis vcfvcfintersect devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect vcflib 1.0.9 (1/1) (1/1) (1/1) (1/1) suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2023.5.0+q2galaxy.2023.5.0.2 (3/3) (3/3) (3/3) (3/3) suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2023.5.0+q2galaxy.2023.5.0.2 (4/5) (4/5) (4/5) (2/5) suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2023.5.1+q2galaxy.2023.5.0.2 (4/4) (4/4) (4/4) (4/4) @@ -286,6 +1115,99 @@ suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiim suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2023.5.0+dist.h193f7cc9.2 (2/2) (2/2) (2/2) (2/2) suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) +ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 (0/1) (1/1) (1/1) (0/1) +appendfdr append_fdr To update appendfdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0.2.0 (0/1) (0/1) (0/1) (0/1) +bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) (0/1) +blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) (0/1) +bumbershoot idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch To update http://proteowizard.sourceforge.net/ Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 (0/5) (0/5) (5/5) (0/5) +calisp calisp Calgary approach to isotopes in proteomics Up-to-date https://github.com/kinestetika/Calisp/ Proteomics calisp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 3.0.13 calisp 3.0.13 (0/1) (0/1) (1/1) (0/1) +cardinal cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets To update http://cardinalmsi.org Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 2.10.0 bioconductor-cardinal 3.4.3 (0/11) (9/11) (11/11) (11/11) +dbbuilder 4758.0 161.0 dbbuilder Protein Database Downloader To update https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder Proteomics dbbuilder galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder 0.3.4 wget (0/1) (1/1) (1/1) (1/1) +decoyfasta 104.0 15.0 Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. To update Proteomics decoyfasta galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta (0/1) (0/1) (0/1) (0/1) +dia_umpire 33.0 2.0 dia_umpire_se DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics To update http://diaumpire.sourceforge.net/ Proteomics dia_umpire galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire 2.1.3 dia_umpire 2.1.6 (0/1) (1/1) (1/1) (0/1) +dialignr 40.0 1.0 dialignr DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. To update https://github.com/shubham1637/DIAlignR Proteomics dialignr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr 1.2.0 bioconductor-dialignr 2.10.0 (0/1) (0/1) (1/1) (0/1) +diann 15.0 3.0 diann DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. To update https://github.com/vdemichev/DiaNN Proteomics diann galaxyp https://github.com/vdemichev/DiaNN https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann 1.8.1 (0/1) (1/1) (1/1) (0/1) +diapysef 245.0 11.0 diapysef diapysef is a convenience package for working with DIA-PASEF data To update https://pypi.org/project/diapysef/ Proteomics diapysef galaxyp https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef 0.3.5.0 diapysef 1.0.10 (0/1) (1/1) (1/1) (0/1) +diffacto 7.0 5.0 diffacto Diffacto comparative protein abundance estimation To update https://github.com/statisticalbiotechnology/diffacto Proteomics diffacto galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto 1.0.6 diffacto 1.0.7 (0/1) (0/1) (1/1) (0/1) +digestdb digestdb To update digestdb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +directag_and_tagrecon To update directag_and_tagrecon galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon (0/1) (0/1) (0/1) (0/1) +data_manager_eggnog_mapper 9.0 2.0 downloads eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper (0/1) (0/1) (0/1) (0/1) +data_manager_eggnog_mapper_abspath 1.0 download eggnog data for eggnog-mapper To update Proteomics data_manager_eggnog_mapper_abspath galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath (0/1) (0/1) (0/1) (0/1) +eggnog_mapper 30565.0 510.0 eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search eggnog-mapper fast functional annotation of novel sequences eggnog-mapper-v2 eggnog-mapper-v2 eggNOG-mapper v2 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis To update Proteomics eggnog_mapper galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper 2.1.8 eggnog-mapper 2.1.12 (3/3) (3/3) (3/3) (3/3) +encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis To update https://bitbucket.org/searleb/encyclopedia/wiki/Home Proteomics encyclopedia galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 1.12.34 encyclopedia 2.12.30 (2/7) (4/7) (7/7) (0/7) +fasta_merge_files_and_filter_unique_sequences 29886.0 461.0 fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together To update https://github.com/galaxyproteomics/tools-galaxyp/ Fasta Manipulation fasta_merge_files_and_filter_unique_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1.2.0 python (1/1) (1/1) (1/1) (1/1) +fastg2protlib 28.0 1.0 fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG To update https://github.com/galaxyproteomics/fastg2protlib.git Proteomics fastg2protlib galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 1.0.2 (0/2) (0/2) (2/2) (0/2) +feature_alignment 18.0 1.0 feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy Up-to-date Proteomics feature_alignment galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0.11.0 msproteomicstools 0.11.0 (0/1) (0/1) (1/1) (0/1) +filter_by_fasta_ids 26274.0 426.0 filter_by_fasta_ids Filter FASTA on the headers and/or the sequences To update Fasta Manipulation, Proteomics filter_by_fasta_ids galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 2.3 python (1/1) (1/1) (1/1) (1/1) +flashlfq 645.0 17.0 flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. Label-free quantification Proteomics experiment, Proteomics To update https://github.com/smith-chem-wisc/FlashLFQ Proteomics flashlfq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq 1.0.3.1 flashlfq 1.2.6 (0/1) (1/1) (1/1) (0/1) +gffcompare_to_bed 2115.0 131.0 gffcompare_to_bed Filter and convert a gffCompare GTF to BED To update https://github.com/gpertea/gffcompare/ Convert Formats gffcompare_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 0.2.1 python (1/1) (1/1) (1/1) (0/1) +hardklor 111.0 2.0 hardklor, kronik Hardklör To update Proteomics hardklor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 2.30.1+galaxy1 hardklor 2.3.2 (0/2) (0/2) (2/2) (0/2) +idconvert 122.0 3.0 idconvert Convert mass spectrometry identification files on linux or MacOSX To update Proteomics idconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert proteowizard 3_0_9992 (0/1) (0/1) (1/1) (0/1) +lfq_protein_quant 111.0 3.0 lfq_protein_quant Enable protein summarisation and quantitation To update https://github.com/compomics/LFQ_galaxy_p Proteomics lfq_protein_quant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 1.0 bioconductor-msnbase 2.28.1 (0/1) (0/1) (1/1) (0/1) +ltq_iquant_cli To update ltq_iquant_cli galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli (0/1) (0/1) (0/1) (0/1) +maldiquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. To update http://strimmerlab.org/software/maldiquant/ Proteomics MALDIquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 1.22.0 r-base (0/2) (2/2) (2/2) (2/2) +map_peptides_to_bed 41.0 1.0 map_peptides_to_bed Map peptides to a reference genome for display by a genome browser To update Proteomics map_peptides_to_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0.2 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +maxquant 5804.0 407.0 maxquant, maxquant_mqpar wrapper for MaxQuant maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Proteomics experiment, Proteomics, Statistics and probability Up-to-date https://www.maxquant.org/ Proteomics maxquant galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant 2.0.3.0 maxquant 2.0.3.0 (2/2) (2/2) (2/2) (0/2) +meta_proteome_analyzer 123.0 10.0 meta_proteome_analyzer MetaProteomeAnalyzer Up-to-date https://github.com/compomics/meta-proteome-analyzer/ Proteomics meta_proteome_analyzer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 2.0.0 mpa-portable 2.0.0 (0/1) (0/1) (1/1) (0/1) +metagene_annotator 636.0 115.0 metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage metageneannotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Up-to-date http://metagene.nig.ac.jp/ Sequence Analysis metagene_annotator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator 1.0 metagene_annotator 1.0 (0/1) (0/1) (1/1) (0/1) +metanovo 4181.0 15.0 metanovo Produce targeted databases for mass spectrometry analysis. Up-to-date https://github.com/uct-cbio/proteomics-pipelines Proteomics metanovo galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo 1.9.4 metanovo 1.9.4 (0/1) (0/1) (1/1) (0/1) +metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function metaQuantome metaQuantome metaQuantome metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Up-to-date https://github.com/galaxyproteomics/metaquantome/ Proteomics metaquantome galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome 2.0.2 metaquantome 2.0.2 (0/6) (6/6) (6/6) (0/6) +mgf_formatter mgf_formatter Up-to-date mgf_formatter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 1.0.0 mgf-formatter 1.0.0 (0/1) (0/1) (0/1) (0/1) +moFF proteomics_moff moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. Up-to-date https://github.com/compomics/moFF Proteomics proteomics_moff galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF 2.0.3 moff 2.0.3 (0/1) (1/1) (1/1) (0/1) +morpheus 140.0 4.0 morpheus Morpheus MS Search Application To update Proteomics morpheus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus 2.255.0 morpheus 288 (0/1) (1/1) (1/1) (0/1) +mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA To update https://github.com/galaxyproteomics/tools-galaxyp/ Proteomics mqppep galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0.1.19 bioconductor-preprocesscore 1.64.0 (0/2) (0/2) (2/2) (0/2) +msconvert 20406.0 190.0 msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container msconvert msconvert msConvert msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. Filtering, Formatting Proteomics, Proteomics experiment To update http://proteowizard.sourceforge.net/tools.shtml Proteomics msconvert galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert 3.0.20287 (1/1) (1/1) (1/1) (1/1) +msgfplus 507.0 5.0 msgfplus MSGF+ To update Proteomics msgfplus galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0.5 msgf_plus 2024.03.26 (0/1) (0/1) (1/1) (0/1) +msms_extractor 110.0 1.0 msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. To update Proteomics msms_extractor galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 1.0.0 proteowizard 3_0_9992 (0/1) (0/1) (1/1) (1/1) +msstats 2036.0 144.0 msstats MSstats tool for analyzing mass spectrometry proteomic datasets msstatstmt msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression To update https://github.com/MeenaChoi/MSstats Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats 4.0.0 bioconductor-msstats 4.10.0 (1/1) (1/1) (1/1) (0/1) +msstatstmt 726.0 71.0 msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling To update http://msstats.org/msstatstmt/ Proteomics msstatstmt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 2.0.0 bioconductor-msstatstmt 2.10.0 (0/1) (1/1) (1/1) (0/1) +mt2mq 270.0 19.0 mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome To update Proteomics mt2mq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 1.1.0 r-tidyverse (0/1) (0/1) (1/1) (0/1) +mz_to_sqlite 844.0 33.0 mz_to_sqlite Creates a SQLite database for proteomics data mztosqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite database Conversion, Peptide database search Proteomics, Biological databases To update https://github.com/galaxyproteomics/mzToSQLite Proteomics mz_to_sqlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite 2.1.1+galaxy0 mztosqlite 2.1.1 (1/1) (1/1) (1/1) (0/1) +openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses To update https://www.openms.de/ Proteomics openms galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 2.8 openms 3.1.0 (8/164) (35/164) (160/164) (0/164) +pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher To update https://github.com/LuisFranciscoHS/PathwayMatcher Proteomics reactome_pathwaymatcher galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher pathwaymatcher 1.9.1 (0/1) (0/1) (1/1) (0/1) +pep_pointer 498.0 9.0 pep_pointer PepPointer categorizes peptides by their genomic coordinates. To update Genomic Interval Operations, Proteomics pep_pointer galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 0.1.3+galaxy1 python (1/1) (1/1) (1/1) (0/1) +pepquery 4862.0 23.0 pepquery A peptide-centric MS search engine for novel peptide identification and validation. To update https://pepquery.org Proteomics pepquery galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1.6.2 pepquery 2.0.2 (0/1) (0/1) (1/1) (0/1) +pepquery2 707.0 10.0 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation Up-to-date https://pepquery.org Proteomics pepquery2 galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 2.0.2 pepquery 2.0.2 (0/3) (0/3) (3/3) (0/3) +peptide_genomic_coordinate 468.0 9.0 peptide_genomic_coordinate Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files To update Proteomics peptide_genomic_coordinate galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate 1.0.0 python (1/1) (1/1) (1/1) (0/1) +peptideshaker 17477.0 485.0 fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker and SearchGUI To update http://compomics.github.io Proteomics peptideshaker galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker searchgui 4.3.6 (4/4) (4/4) (4/4) (4/4) +pepxml_to_xls Convert PepXML to Tabular To update Proteomics pepxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls (0/1) (0/1) (0/1) (0/1) +percolator 368.0 5.0 batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator Up-to-date Proteomics percolator galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 3.5 percolator 3.5 (0/4) (4/4) (4/4) (0/4) +pi_db_tools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools To update Proteomics hirieftools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 1.3 python (0/3) (0/3) (0/3) (0/3) +pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS To update https://github.com/slhubler/PMD-FDR-for-Galaxy-P Proteomics pmd_fdr galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 1.4.0 r-base (0/1) (0/1) (0/1) (0/1) +custom_pro_db 1652.0 57.0 custom_pro_db CustomProDB To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1.22.0 bioconductor-rgalaxy 1.37.1 (1/1) (1/1) (1/1) (1/1) +custom_pro_db_annotation_data_manager CustomProDB Annotation To update https://bioconductor.org/packages/release/bioc/html/customProDB.html Proteomics custom_pro_db_annotation_data_manager galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager (0/1) (0/1) (0/1) (0/1) +psm2sam PSMtoSAM PSM to SAM To update https://bioconductor.org/packages/release/bioc/html/proBAMr.html Proteomics psm_to_sam galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam 1.3.2.1 r-base (0/1) (0/1) (0/1) (1/1) +proteinpilot convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml To update proteinpilot galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot 0.1 (0/5) (0/5) (0/5) (0/5) +retrieve_ensembl_bed retrieve_ensembl_bed Retrieve cDNA features from Ensembl REST API in BED format To update http://rest.ensembl.org/ Data Source retrieve_ensembl_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed 0.1.0 (0/1) (0/1) (0/1) (0/1) +translate_bed 643.0 49.0 translate_bed Translate BED transcript CDS or cDNA in 3 frames To update http://rest.ensembl.org/ Proteomics translate_bed galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 0.1.0 (1/1) (1/1) (1/1) (0/1) +proteomiqon_joinquantpepionswithproteins 366.0 4.0 proteomiqon_joinquantpepionswithproteins The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. To update https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html Proteomics proteomiqon_joinquantpepionswithproteins galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins 0.0.1 proteomiqon-joinquantpepionswithproteins 0.0.2 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labeledproteinquantification 14.0 5.0 proteomiqon_labeledproteinquantification The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html Proteomics proteomiqon_labeledproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification 0.0.1 proteomiqon-labeledproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_labelfreeproteinquantification 6.0 3.0 proteomiqon_labelfreeproteinquantification The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. To update https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html Proteomics proteomiqon_labelfreeproteinquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification 0.0.1 proteomiqon-labelfreeproteinquantification 0.0.3 (0/1) (0/1) (1/1) (0/1) +proteomiqon_mzmltomzlite 721.0 5.0 proteomiqon_mzmltomzlite The tool MzMLToMzLite allows to convert mzML files to mzLite files. Up-to-date https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html Proteomics proteomiqon_mzmltomzlite galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite 0.0.8 proteomiqon-mzmltomzlite 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidedb 96.0 6.0 proteomiqon_peptidedb The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html Proteomics proteomiqon_peptidedb galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb 0.0.7 proteomiqon-peptidedb 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_peptidespectrummatching 686.0 4.0 proteomiqon_peptidespectrummatching Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html Proteomics proteomiqon_peptidespectrummatching galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching 0.0.7 proteomiqon-peptidespectrummatching 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_proteininference 89.0 4.0 proteomiqon_proteininference MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. Up-to-date https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html Proteomics proteomiqon_proteininference galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference 0.0.7 proteomiqon-proteininference 0.0.7 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmbasedquantification 604.0 4.0 proteomiqon_psmbasedquantification The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. To update https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html Proteomics proteomiqon_psmbasedquantification galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification 0.0.8 proteomiqon-psmbasedquantification 0.0.9 (0/1) (0/1) (1/1) (0/1) +proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. Up-to-date https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html Proteomics proteomiqon_psmstatistics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics 0.0.8 proteomiqon-psmstatistics 0.0.8 (0/1) (0/1) (1/1) (0/1) +proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram 2021.06.08 python (0/1) (0/1) (0/1) (0/1) +protxml_to_xls protxml_to_xls To update protxml_to_xls galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls 0.1.0 trans_proteomic_pipeline (0/1) (0/1) (0/1) (0/1) +psm_eval psm_eval To update psm_eval galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval 0.1.0 binaries_for_psm_eval (0/1) (0/1) (0/1) (0/1) +psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) (0/1) +pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) (0/6) +pyteomics mztab2tsv Tools using the pyteomics library pyteomics pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7.1 (0/1) (0/1) (1/1) (0/1) +quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) (1/1) +quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) (0/1) +qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter 0.2.0 geojson (0/1) (0/1) (1/1) (0/1) +rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) (0/1) +regex_find_replace 60307.0 495.0 regex1, regexColumn1 Use python regular expressions to find and replace text To update Text Manipulation regex_find_replace galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 1.0.3 python (2/2) (2/2) (2/2) (2/2) +scaffold scaffold, scaffold_export To update scaffold galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0.1.0 scaffold (0/2) (0/2) (0/2) (0/2) +sixgill 293.0 24.0 sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS Up-to-date Proteomics, MetaProteomics sixgill galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0.2.4 sixgill 0.2.4 (0/4) (0/4) (4/4) (0/4) +spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files To update Proteomics spectrast2spectrast_irt galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files To update Proteomics spectrast2tsv galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0.1.0 msproteomicstools 0.11.0 (0/1) (0/1) (0/1) (0/1) +translate_bed_sequences 57.0 6.0 translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column To update Proteomics translate_bed_sequences galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0.2.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) +unipept 5005.0 115.0 unipept Unipept retrieves metaproteomics information unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows To update https://github.com/galaxyproteomics/tools-galaxyp Proteomics unipept galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept 4.5.1 python (1/1) (1/1) (1/1) (0/1) +uniprotxml_downloader 1360.0 79.0 uniprotxml_downloader Download UniProt proteome in XML or fasta format To update Proteomics uniprotxml_downloader galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 2.4.0 requests (0/1) (1/1) (1/1) (0/1) +validate_fasta_database 86.0 25.0 validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. To update Fasta Manipulation, Proteomics validate_fasta_database galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 0.1.5 validate-fasta-database 1.0 (0/1) (0/1) (1/1) (0/1) bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. To update http://thegrantlab.org/bio3d/index.php Computational chemistry bio3d chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 2.4_1 r-bio3d 2.3_3 (5/5) (4/5) (5/5) (0/5) biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis To update https://github.com/moldyn/ Molecular Dynamics, Computational chemistry biomoldyn chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 1.5.2 scipy (4/4) (0/4) (4/4) (0/4) ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. To update http://ambermd.org/AmberTools.php Molecular Dynamics, Computational chemistry ambertools chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 21.10 ambertools (7/7) (2/7) (7/7) (0/7) @@ -299,7 +1221,7 @@ mdslicer md_slicer A tool for slicing trajectory files using MDTraj. To mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories To update https://github.com/mdtraj/mdtraj Computational chemistry mdtraj chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1.9.7 mdtraj (1/1) (0/1) (1/1) (0/1) openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performance GPU code. To update https://github.com/openmm Molecular Dynamics, Computational chemistry openmm chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm 1.8.1 pdbfixer (0/1) (0/1) (1/1) (0/1) vmd vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations To update https://www.ks.uiuc.edu/Research/vmd/ Computational chemistry vmd chemteam https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd (0/1) (0/1) (0/1) (0/1) -artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.19.2 (0/1) (0/1) (0/1) (0/1) +artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis To update http://artbio.fr SAM, Variant Analysis artbio_bam_cleaning artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 1.10+galaxy0 samtools 1.20 (0/1) (0/1) (0/1) (0/1) bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.0 (0/1) (0/1) (0/1) (0/1) bigwig_to_bedgraph 5749.0 200.0 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) (0/1) bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format To update https://artbio.fr Convert Formats bigwig_to_wig artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 3+galaxy0 ucsc-bigwiginfo 377 (0/1) (0/1) (0/1) (0/1) @@ -340,6 +1262,7 @@ pathifier 228.0 10.0 pathifier pathifier Up-to-date https:// Transcriptom pindel pindel Pindel detects genome-wide structural variation. Up-to-date http://artbio.fr Variant Analysis pindel artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0.2.5b9 pindel 0.2.5b9 (0/1) (0/1) (0/1) (0/1) probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets Up-to-date http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage 0.22.0 pysam 0.22.0 (0/1) (0/1) (0/1) (0/1) repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 (0/2) (2/2) (0/2) (0/2) +repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 (0/2) (0/2) (0/2) (0/2) rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) (0/4) sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM To update http://artbio.fr SAM sambamba artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0.7.1+galaxy1 sambamba 1.0 (0/1) (1/1) (0/1) (0/1) sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python (0/1) (0/1) (0/1) (0/1) @@ -399,7 +1322,7 @@ salmon-kallisto-mtx-to-10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 (0/8) (0/8) (6/8) (0/8) data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 (0/1) (0/1) (1/1) (0/1) data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget (1/1) (1/1) (1/1) (0/1) -decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/decoupler 1.4.0+galaxy1 decoupler 1.5.0 (0/3) (0/3) (1/3) (0/3) +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 (0/3) (0/3) (1/3) (0/3) dropletutils 3934.0 126.0 dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 (2/2) (0/2) (2/2) (0/2) garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 (0/7) (0/7) (7/7) (0/7) monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 (9/9) (0/9) (9/9) (0/9) @@ -412,6 +1335,27 @@ scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_prepr scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) (0/4) seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (14/19) (0/19) ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.5 (0/1) (0/1) (1/1) (0/1) +biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) (1/1) +filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1) +gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 (0/1) (0/1) (0/1) (0/1) +matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.24.0 matchms 0.24.4 (2/13) (9/13) (13/13) (11/13) +misc use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 (0/1) (0/1) (1/1) (0/1) +msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 (0/1) (1/1) (1/1) (1/1) +msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.24.4 (0/1) (0/1) (0/1) (0/1) +mzml_validator mzml_validator mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. To update https://github.com/RECETOX/galaxytools Metabolomics, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator 0.1.0+galaxy2 lxml (0/1) (0/1) (0/1) (0/1) +qcxms qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). To update https://github.com/grimme-lab/QCxMS Computational chemistry, Molecular Dynamics QCxMS recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 5.2.1 (0/3) (0/3) (3/3) (0/3) +query query Execute an SQL statement on a set of tables To update Text Manipulation query recetox https://github.com/RECETOX/galaxytools/tree/master/tools/query https://github.com/RECETOX/galaxytools/tree/master/tools/query 0.2 click (0/1) (0/1) (0/1) (0/1) +ramclustr 15.0 2.0 ramclustr, ramclustr_define_experiment ramclustr ramclustr RAMClustR A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. Imputation, Standardisation and normalisation, Clustering, Correlation Metabolomics To update https://rdrr.io/cran/RAMClustR/ Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr 1.3.0 r-ramclustr 1.3.1 (2/2) (2/2) (2/2) (2/2) +recetox_aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. recetox-aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Up-to-date https://github.com/RECETOX/recetox-aplcms Metabolomics recetox-aplcms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms 0.12.0 r-recetox-aplcms 0.12.0 (0/8) (8/8) (8/8) (8/8) +recetox_msfinder recetox_msfinder recetox-msfinder recetox-msfinder recetox-msfinder This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Annotation Metabolomics To update https://github.com/RECETOX/recetox-msfinder Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder v3.5.2 (0/1) (0/1) (1/1) (1/1) +recetox_xmsannotator recetox_xmsannotator_advanced recetox-xmsannotator recetox-xmsannotator recetox-xMSannotator Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation Up-to-date https://github.com/RECETOX/recetox-xMSannotator Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator 0.10.0 r-recetox-xmsannotator 0.10.0 (0/1) (1/1) (1/1) (1/1) +rem_complex rem_complex Removes molecular coordination complexes. To update https://github.com/RECETOX/galaxytools Metabolomics rem_complex recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 1.0.0 pandas (0/1) (0/1) (1/1) (0/1) +retip retip_apply, retip_descriptors, retip_filter_rt, retip_train retip retip Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry To update https://github.com/PaoloBnn/Retip Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/retip https://github.com/RECETOX/galaxytools/tree/master/tools/retip 0.5.4 (0/4) (0/4) (0/4) (0/4) +riassigner 15.0 3.0 riassigner, riassigner_from_comment riassigner riassigner RIAssigner RIAssigner is a python tool for retention index (RI) computation for GC-MS data. Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/RIAssigner Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner 0.4.0 riassigner 0.4.0 (1/2) (0/2) (2/2) (1/2) +rmassbank rmassbank RMassBank is an R package for processing tandem MS files and building of MassBank records. To update https://github.com/MassBank/RMassBank Metabolomics rmassbank recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank 3.0.0 python (0/1) (1/1) (1/1) (1/1) +spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Up-to-date https://github.com/iomega/spec2vec Metabolomics spec2vec recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec 0.8.0 spec2vec 0.8.0 (0/2) (0/2) (0/2) (0/2) +waveica 6.0 waveica Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. waveica waveica WaveICA Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. Standardisation and normalisation Metabolomics Up-to-date https://github.com/RECETOX/WaveICA Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/waveica https://github.com/RECETOX/galaxytools/tree/master/tools/waveica 0.2.0 r-recetox-waveica 0.2.0 (1/1) (0/1) (1/1) (1/1) +xtb xtb_molecular_optimization Performs semiempirical molecular optimization. To update https://github.com/grimme-lab/xtb Metabolomics xtb_molecular_optimization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 6.6.1 xtb (0/1) (0/1) (1/1) (1/1) consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis consolidate_vcfs nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) filter_density filterdensity Filter out position based on distance between SNVs Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_density nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) filter_stats filterstat SNVPhyl filter_stats Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis filter_stats nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) @@ -423,7 +1367,7 @@ snv_matrix snvmatrix Generate matrix of SNV distances Up-to-date https: vcf2snvalignment vcf2snvalignment Generates multiple alignment of variant calls Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis vcf2snvalignment nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) verify_map verify_map Checks the mapping quality of all BAM(s) Up-to-date https://snvphyl.readthedocs.io/en/latest/ Sequence Analysis verify_map nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map 1.8.2 snvphyl-tools 1.8.2 (0/1) (0/1) (0/1) (0/1) suite_snvphyl SNVPhyl suite defining all dependencies for SNVPhyl To update Sequence Analysis suite_snvphyl_1_2_3 nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl (0/1) (0/1) (0/1) (0/1) -cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.19.1 (4/5) (0/5) (4/5) (0/5) +cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab To update https://github.com/open2c/cooler Epigenetics cooler lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 0.9.3 htslib 1.20 (4/5) (0/5) (4/5) (0/5) fromHicupToJuicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. To update Epigenetics from_hicup_to_juicebox lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) (0/1) fromgtfTobed12 fromgtfTobed12 Convert GTF files to BED12 format To update https://pythonhosted.org/gffutils/contents.html Convert Formats fromgtftobed12 lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0.11.1+galaxy1 gffutils 0.13 (0/1) (0/1) (0/1) (0/1) getTn5ExtendedCoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension To update Epigenetics gettn5extendedcoverage lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0.0.2 pysam 0.22.0 (0/1) (0/1) (0/1) (0/1) @@ -434,7 +1378,7 @@ omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) (0/1) omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20231211 (0/1) (0/1) (0/1) (0/1) -revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.19.2 (1/1) (0/1) (1/1) (0/1) +revertR2orientationInBam revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. To update SAM revertr2orientationinbam lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam 0.0.2 samtools 1.20 (1/1) (0/1) (1/1) (0/1) upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) blast2go 1232.0 101.0 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1) (0/1) blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh Fasta Manipulation, Sequence Analysis blast_rbh peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 (0/1) (0/1) (1/1) (0/1) diff --git a/results/all_tools_wordcloud.png b/results/all_tools_wordcloud.png index 218af4cd..8abfe3ef 100644 Binary files a/results/all_tools_wordcloud.png and b/results/all_tools_wordcloud.png differ