diff --git a/results/imaging/index.html b/results/imaging/index.html index 1f3b1ef2..b5d1e40e 100644 --- a/results/imaging/index.html +++ b/results/imaging/index.html @@ -821,16 +821,16 @@ superdsm 0.1.3 - 0.1.3 + 0.2.0 superdsm - Up-to-date + To update superdsm SuperDSM Image analysis Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. - Up-to-date + To update https://github.com/bmcv Imaging superdsm @@ -940,7 +940,7 @@ graphicsmagick - 1.3.40 + 1.3.42 1.3.26 graphicsmagick To update diff --git a/results/imaging/tools.tsv b/results/imaging/tools.tsv index 902f25bb..be75f930 100644 --- a/results/imaging/tools.tsv +++ b/results/imaging/tools.tsv @@ -36,13 +36,13 @@ segmetrics 3.0 2.0 ip_segmetrics Image segmentation and object detection perform slice_image 102.0 ip_slice_image Slice image galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging slice_image imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ 0.3-2 scikit-image (0/1) (0/1) (1/1) False split_labelmap 42.0 ip_split_labelmap Split Labelmaps galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/bmcv Imaging split_labelmap imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False spot_detection_2d 16.0 3.0 ip_spot_detection_2d Spot detection in 2D image sequence galaxy_image_analysis Galaxy Image Analysis Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg. Image analysis Imaging, Bioinformatics To update https://github.com/BMCV/galaxy-image-analysis Imaging spot_detection_2d imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ 0.0.3-2 imageio (0/1) (0/1) (1/1) False -superdsm 16.0 2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis Up-to-date https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.1.3 (0/1) (0/1) (1/1) False +superdsm 16.0 2.0 ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. Image analysis To update https://github.com/bmcv Imaging superdsm imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ 0.1.3 superdsm 0.2.0 (0/1) (0/1) (1/1) False visceral-evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool To update https://github.com/bmcv Imaging visceral_evaluatesegmentation imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation 0.5-2 visceral-evaluatesegmentation 2015.07.03 (0/1) (0/1) (1/1) False wsi_extract_top_view 38.0 ip_wsi_extract_top_view WSI Extract Top View To update https://github.com/bmcv Imaging wsi_extract_top_view imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ 0.2-2 scikit-image (0/1) (0/1) (1/1) False cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools (0/23) (23/23) (23/23) False cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools 4.2.6 (0/1) (0/1) (1/1) False bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools 0.1.0 wget (0/1) (0/1) (1/1) False -graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.40 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) False +graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ 1.3.42 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) False imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) False spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) False qupath_roi_splitter 59.0 5.0 qupath_roi_splitter Split ROI coordinates of QuPath TMA annotation by cell type To update https://github.com/npinter/ROIsplitter Imaging qupath_roi_splitter galaxyp hhttps://github.com/npinter/ROIsplitter 0.1.0+galaxy1 geojson (0/1) (0/1) (1/1) False diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html index 0c96dc24..b423edbd 100644 --- a/results/microgalaxy/index.html +++ b/results/microgalaxy/index.html @@ -621,7 +621,7 @@ gi2taxonomy 1.1.1 - 0.9.0 + 0.10.0 taxonomy To update @@ -661,7 +661,7 @@ lca_wrapper 1.0.1 - 0.9.0 + 0.10.0 taxonomy To update @@ -681,7 +681,7 @@ t2ps 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -701,7 +701,7 @@ t2t_report 1.0.0 - 0.9.0 + 0.10.0 taxonomy To update @@ -1361,16 +1361,16 @@ amrfinderplus 3.11.26 - 3.11.26 + 3.12.8 ncbi-amrfinderplus - Up-to-date + To update amrfinderplus AMRFinderPlus Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms - Up-to-date + To update https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus @@ -1420,17 +1420,17 @@ bakta - 1.8.2 + 1.9.2 1.9.2 bakta - To update + Up-to-date Bakta Bakta Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." Rapid & standardized annotation of bacterial genomes, MAGs & plasmids - To update + Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta @@ -1504,12 +1504,12 @@ 2.1.7 biom-format To update - - - - + biomformat + biomformat + Formatting + Laboratory information management, Sequence analysis The biom-format package provides a command line interface and Python API for working with BIOM files. - + This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. To update https://github.com/biocore/biom-format Metagenomics @@ -1557,6 +1557,26 @@ iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ + + + cactus + 2.7.1 + + + To update + cactus + Cactus + Multiple sequence alignment, Genome alignment + Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics + Cactus is a reference-free whole-genome multiple alignment program + Cactus is a reference-free whole-genome multiple alignment program. + To update + https://github.com/ComparativeGenomicsToolkit/cactus + Sequence Analysis + cactus + galaxy-australia + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus + cat @@ -1664,12 +1684,12 @@ 4.10.7 paml To update - - - - + paml + PAML + Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis + Phylogenetics, Sequence analysis Detects positive selection - + Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics @@ -1801,7 +1821,7 @@ diamond 2.0.15 - 2.1.8 + 2.1.9 diamond To update diamond @@ -1844,12 +1864,12 @@ 1.4.6 dram To update - - - - + dram + DRAM + Gene functional annotation + Metagenomics, Biological databases, Molecular genetics DRAM for distilling microbial metabolism to automate the curation of microbiome function - + Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes To update https://github.com/WrightonLabCSU/DRAM Metagenomics @@ -1884,12 +1904,12 @@ 0.22 export2graphlan To update - - - - + export2graphlan + export2graphlan + Conversion + Taxonomy, Metabolomics, Biomarkers export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn - + export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics @@ -1904,12 +1924,12 @@ 0.1 fargene Up-to-date - - - - + fargene + fARGene + Antimicrobial resistance prediction + Metagenomics, Microbiology, Public health and epidemiology fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) - + fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. Up-to-date https://github.com/fannyhb/fargene Sequence Analysis @@ -1944,14 +1964,14 @@ 0.3.1 fastqe To update - - - - + fastqe FASTQE - + Sequencing quality control + Sequence analysis, Sequencing + FASTQE + Compute quality stats for FASTQ files and print those stats as emoji... for some reason. To update - https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe + https://fastqe.com/ Sequence Analysis fastqe iuc @@ -2021,7 +2041,7 @@ freyja 1.4.4 - 1.4.8 + 1.4.9 freyja To update freyja @@ -2124,14 +2144,14 @@ 1.1.3 graphlan To update - - - - + graphlan + GraPhlAn + Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification + Metagenomics, Phylogenetics, Phylogenomics, Cladistics GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees - + GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. To update - https://bitbucket.org/nsegata/graphlan/overview + https://github.com/biobakery/graphlan Metagenomics, Graphics, Phylogenetics graphlan iuc @@ -2144,12 +2164,12 @@ 2.3.2 gtdbtk To update - - - - + GTDB-Tk + GTDB-Tk + Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval + Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. - + a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). To update https://github.com/Ecogenomics/GTDBTk Metagenomics @@ -2161,7 +2181,7 @@ gubbins 3.2.1 - 3.3.1 + 3.3.3 gubbins To update gubbins @@ -2184,12 +2204,12 @@ 1.1.4 hamronization To update - - - - + hamronization + hAMRonization + Data handling, Antimicrobial resistance prediction, Parsing + Public health and epidemiology, Microbiology, Bioinformatics Convert AMR gene detection tool output to hAMRonization specification format. - + Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure To update https://github.com/pha4ge/hAMRonization Sequence Analysis @@ -2224,12 +2244,12 @@ hamtv0.3.1 hifiasm_meta To update - - - - + hifiasm-meta + Hifiasm-meta + Sequence assembly + Sequence assembly, Metagenomics A hifiasm fork for metagenome assembly using Hifi reads. - + Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics @@ -2324,12 +2344,12 @@ 1.3.1 icescreen Up-to-date - - - - + icescreen + ICEscreen + Database search, Protein feature detection + Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. - + A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation @@ -2461,7 +2481,7 @@ jellyfish - 2.3.0 + 2.3.1 kmer-jellyfish To update Jellyfish @@ -2901,7 +2921,7 @@ megan 6.21.7 - 6.24.20 + 6.25.9 megan To update megan @@ -3464,12 +3484,12 @@ 1.46.0 bioconductor-phyloseq To update - - - - + phyloseq + phyloseq + Deposition, Analysis, Visualisation + Microbiology, Sequence analysis, Metagenomics Handling and analysis of high-throughput microbiome census data - + Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics @@ -3504,12 +3524,12 @@ 1.1.4 picrust To update - - - - + picrust + PICRUSt + Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding + Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing PICRUSt wrappers - + PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. To update https://picrust.github.io/picrust/ Metagenomics @@ -3801,16 +3821,16 @@ recentrifuge 1.13.2 - 1.13.2 + 1.14.0 recentrifuge - Up-to-date + To update Recentrifuge Recentrifuge Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." Robust comparative analysis and contamination removal for metagenomics. - Up-to-date + To update https://github.com/khyox/recentrifuge Metagenomics recentrifuge @@ -3941,7 +3961,7 @@ seqkit 2.3.1 - 2.6.1 + 2.7.0 seqkit To update seqkit @@ -4484,12 +4504,12 @@ 2.1.3 kraken2 To update - - - - + kraken2 + kraken2 + Taxonomic classification + Taxonomy, Metagenomics Kraken2 for taxonomic designation. - + Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics @@ -4537,6 +4557,26 @@ galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator + + + ez_histograms + 3.4.4 + 2.2.1 + r-ggplot2 + To update + + + + + ggplot2 histograms and density plots + + To update + https://github.com/tidyverse/ggplot2 + Visualization, Statistics + ez_histograms + artbio + https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms + Geom_mean_workflow diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv index fcbcc977..cd8052e7 100644 --- a/results/microgalaxy/tools.tsv +++ b/results/microgalaxy/tools.tsv @@ -1,6 +1,6 @@ Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu Reviewed To keep braker 109.0 17.0 braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 2.1.6 (0/1) (0/1) (1/1) True False -braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.6 (0/1) (1/1) (1/1) True False +braker3 567.0 10.0 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . To update https://github.com/Gaius-Augustus/BRAKER Genome annotation braker3 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker 3.0.7 (0/1) (1/1) (1/1) True False helixer 93.0 1.0 helixer Gene calling with Deep Neural Networks To update https://github.com/weberlab-hhu/Helixer Genome annotation helixer genouest https://github.com/genouest/galaxy-tools/tree/master/tools/helixer 0.3.2 (0/1) (0/1) (1/1) True False logol logol_wrapper Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence Up-to-date http://logol.genouest.org/web/app.php/logol Sequence Analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/logol 1.7.8 logol 1.7.8 (0/1) (0/1) (0/1) True False peptimapper peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag Proteogenomics workflow for the expert annotation of eukaryotic genomes To update https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 Proteomics genouest 2.0 (0/4) (0/4) (0/4) True False @@ -99,13 +99,13 @@ weightedaverage wtavg Assign weighted-average of the values of features overla windowsplitter winSplitter Make windows To update Sequence Analysis, Variant Analysis windowsplitter devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 1.0.1 bx-python 0.10.0 (1/1) (0/1) (0/1) True False hgv_fundo hgv_funDo FunDO human genes associated with disease terms To update Sequence Analysis hgv_fundo devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo 1.0.0 (1/1) (0/1) (1/1) True False hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve To update https://www.ebi.ac.uk/huber-srv/hilbert/ Graphics, Visualization hgv_hilbertvis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis 1.0.0 R (1/1) (0/1) (1/1) True False -find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True False -gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True +find_diag_hits 69.0 5.0 find_diag_hits Find diagnostic hits To update https://bitbucket.org/natefoo/taxonomy Metagenomics find_diag_hits devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) True False +gi2taxonomy 660.0 27.0 Fetch Taxonomic Ranks Fetch taxonomic representation To update https://bitbucket.org/natefoo/taxonomy Metagenomics gi2taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy 1.1.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) True True kraken2tax 14683.0 481.0 Kraken2Tax Convert Kraken output to Galaxy taxonomy data. To update https://bitbucket.org/natefoo/taxonomy Metagenomics kraken2tax devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ 1.2+galaxy0 gawk (1/1) (1/1) (1/1) True True -lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.9.0 (0/1) (1/1) (1/1) True False -t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True -t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.9.0 (0/1) (0/1) (1/1) True True +lca_wrapper 137.0 2.0 lca1 Find lowest diagnostic rank To update https://bitbucket.org/natefoo/taxonomy Metagenomics lca_wrapper devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper 1.0.1 taxonomy 0.10.0 (0/1) (0/1) (1/1) True True +poisson2test 116.0 6.0 poisson2test Poisson two-sample test To update https://bitbucket.org/natefoo/taxonomy Statistics, Metagenomics poisson2test devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test 1.0.0 taxonomy 0.10.0 (0/1) (1/1) (1/1) True False +t2ps 457.0 31.0 Draw_phylogram Draw phylogeny To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2ps devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) True True +t2t_report 947.0 26.0 t2t_report Summarize taxonomy To update https://bitbucket.org/natefoo/taxonomy Metagenomics t2t_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report 1.0.0 taxonomy 0.10.0 (0/1) (0/1) (1/1) True True AggregateAlignments graphclust_aggregate_alignments Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. Up-to-date RNA graphclust_aggregate_alignments rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments 0.6.0 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False AlignCluster graphclust_align_cluster Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. To update RNA graphclust_align_cluster rnateam https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster 0.1 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False CMFinder cmFinder Determines consensus motives for sequences. To update RNA graphclust_cmfinder rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder 0.4 graphclust-wrappers 0.6.0 (0/1) (0/1) (1/1) True False @@ -180,7 +180,7 @@ compalignp 220.0 compalignp Compute fractional identity between trusted alignme coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs To update https://github.com/PatrickRWright/CopraRNA RNA, Sequence Analysis coprarna rnateam https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 (0/1) (0/1) (0/1) True False dewseq 72.0 11.0 dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data To update https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers Sequence Analysis, RNA, CLIP-seq dewseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0.1.0+galaxy0 python (0/1) (0/1) (1/1) True False dorina 1086.0 1.0 dorina_search data source for RNA interactions in post-transcriptional regulation To update RNA, Data Source dorina rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ 1.0 (0/1) (0/1) (1/1) True False -dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.3 (0/1) (0/1) (0/1) True False +dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) To update Sequence Analysis, RNA dot2ct rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 5.7.a rnastructure 6.4 (0/1) (0/1) (0/1) True False dotknot 83.0 1.0 dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence To update http://dotknot.csse.uwa.edu.au/ RNA, Proteomics dotknot bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot 1.3.1 vienna_rna (0/1) (0/1) (1/1) True False exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Up-to-date http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp RNA exparna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 1.0.1 exparna 1.0.1 (0/1) (0/1) (0/1) True False graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. To update https://github.com/dmaticzka/GraphProt Sequence Analysis, RNA, CLIP-seq graphprot rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 1.1.7+galaxy1 graphprot 1.1.7 (0/1) (0/1) (1/1) True False @@ -258,9 +258,9 @@ aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEG aldex2 129.0 13.0 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) True True amplican 53.0 12.0 amplican AmpliCan is an analysis tool for genome editing. amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. Alignment, Standardisation and normalisation PCR experiment, Statistics and probability To update https://github.com/valenlab/amplican Sequence Analysis amplican iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican 1.14.0 bioconductor-amplican 1.24.0 (0/1) (0/1) (1/1) True True ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. Analysis, Visualisation Biodiversity To update https://github.com/MadsAlbertsen/ampvis2/ Metagenomics ampvis2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 2.7.22 (0/19) (0/19) (19/19) True False -amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Up-to-date https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.11.26 (0/1) (0/1) (1/1) True True +amrfinderplus 591.0 amrfinderplus """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://github.com/ncbi/amr Sequence Analysis AMRFinderPlus iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus 3.11.26 ncbi-amrfinderplus 3.12.8 (0/1) (0/1) (1/1) True True ancombc 7.0 4.0 ancombc Performs analysis of compositions of microbiomes with bias correction. ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. DNA barcoding Microbial ecology, Metagenomics To update https://github.com/FrederickHuangLin/ANCOMBC Metagenomics ancombc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc 1.4.0 bioconductor-ancombc 2.4.0 (0/1) (0/1) (1/1) True True -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.10.3 anndata 0.6.22.post1 (5/5) (3/5) (5/5) True False +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Transcriptomics, Sequence Analysis anndata iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ 0.10.3 anndata 0.6.22.post1 (5/5) (4/5) (5/5) True False annotatemyids 26115.0 1175.0 annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. Annotation To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids Genome annotation annotatemyids iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.17.0 bioconductor-org.hs.eg.db 3.18.0 (1/1) (1/1) (1/1) True False arriba 3436.0 28.0 arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba 2.4.0 arriba 2.4.0 (0/3) (3/3) (3/3) True False art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD Conversion Bioinformatics To update Sequence Analysis, Data Source art iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art 2014.11.03.0 art 2016.06.05 (0/3) (0/3) (0/3) True False @@ -268,32 +268,33 @@ artic artic_guppyplex, artic_minion The artic pipeline is designed to help run assembly-stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. Up-to-date https://github.com/rjchallis/assembly-stats Assembly assembly_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats 17.02 rjchallis-assembly-stats 17.02 (0/1) (0/1) (0/1) True False augustus 8864.0 516.0 augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families To update http://bioinf.uni-greifswald.de/augustus/ Sequence Analysis augustus bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus 3.4.0 augustus 3.5.0 (2/2) (2/2) (2/2) True False b2btools b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA Protein disorder prediction, Protein secondary structure prediction, Protein feature detection To update https://bio2byte.be Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology iuc 3.0.5+galaxy0 b2btools 3.0.6 (0/1) (0/1) (1/1) True False -bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis To update https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.8.2 bakta 1.9.2 (0/1) (1/1) (1/1) True True +bakta 2982.0 151.0 bakta """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" Bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids Genome annotation Genomics, Data submission, annotation and curation, Sequence analysis Up-to-date https://github.com/oschwengers/bakta Sequence Analysis bakta iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta 1.9.2 bakta 1.9.2 (0/1) (1/1) (1/1) True True bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. To update https://github.com/statgen/bamUtil Sequence Analysis bamutil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil bamutil 1.0.15 (1/2) (1/2) (1/2) True False bandage 44390.0 2016.0 bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. Sequence assembly visualisation Genomics, Sequence assembly Up-to-date https://github.com/rrwick/Bandage Visualization bandage iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage 2022.09 bandage_ng 2022.09 (2/2) (2/2) (2/2) True True baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Transcriptomics, Visualization baredsc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc 1.1.2 baredsc 1.1.2 (4/4) (0/4) (4/4) True False barrnap 3938.0 160.0 barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Gene prediction Genomics, Model organisms, Model organisms To update Sequence Analysis barrnap iuc 1.2.2 barrnap 0.9 (0/1) (1/1) (1/1) True False bax2bam 200.0 8.0 bax2bam BAX to BAM converter Up-to-date https://github.com/pacificbiosciences/bax2bam/ Convert Formats, Sequence Analysis bax2bam iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam 0.0.11 bax2bam 0.0.11 (1/1) (0/1) (1/1) True False bayescan 64.0 8.0 BayeScan Detecting natural selection from population-based genetic data bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism To update http://cmpg.unibe.ch/software/BayeScan/index.html Sequence Analysis bayescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ 2.1 bayescan 2.0.1 (0/1) (0/1) (1/1) True True -bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.01 bbmap 39.01 (1/6) (1/6) (5/6) True False +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. Up-to-date https://jgi.doe.gov/data-and-tools/bbtools/ Sequence Analysis bbtools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools 39.06 bbmap 39.06 (6/6) (1/6) (5/6) True False bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools 0.2.2 bctools 0.2.2 (0/7) (0/7) (7/7) True False bellerophon 1194.0 123.0 bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. Up-to-date https://github.com/davebx/bellerophon Sequence Analysis bellerophon iuc https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 (1/1) (1/1) (1/1) True False binning_refiner 81.0 21.0 bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs Read binning, Sequence clustering Metagenomics Up-to-date https://github.com/songweizhi/Binning_refiner Metagenomics binning_refiner iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ 1.4.3 binning_refiner 1.4.3 (0/1) (0/1) (1/1) True True bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics To update https://github.com/dariober/bioinformatics-cafe/ Sequence Analysis bioinformatics_cafe mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe 0.1.0 python (1/1) (0/1) (1/1) True False -biom_format biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. To update https://github.com/biocore/biom-format Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) True True +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 "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 2.1.15 biom-format 2.1.7 (2/6) (2/6) (1/6) True True bioperl bp_genbank2gff3 Converts GenBank format files to GFF3 bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. Data handling, Service invocation Genomics, Software engineering, Data management To update https://bioperl.org/ Sequence Analysis bp_genbank2gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl 1.1 perl-bioperl 1.7.8 (1/1) (1/1) (1/1) True False biscot 3.0 1.0 biscot Bionano scaffolding correction tool Up-to-date https://github.com/institut-de-genomique/biscot Assembly biscot iuc https://github.com/bgruening/iuc/tree/master/tools/biscot 2.3.3 biscot 2.3.3 (0/1) (0/1) (1/1) True False blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 To update Convert Formats, Sequence Analysis blastxml_to_gapped_gff3 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 (1/1) (1/1) (1/1) True False bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken 2.9 bracken 2.9 (0/1) (0/1) (1/1) True True busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ 5.5.0 busco 5.6.1 (1/1) (1/1) (1/1) True True bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) True False +cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program 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 2.7.1 (0/2) (2/2) (2/2) False calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) True False cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) True True cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) True True cemitool 98.0 9.0 cemitool Gene co-expression network analysis tool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment To update https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool 1.18.1 bioconductor-cemitool 1.26.0 (1/1) (0/1) (1/1) True True charts 3589.0 287.0 charts Enables advanced visualization options in Galaxy Charts To update Visualization charts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt (0/1) (0/1) (0/1) True False checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Operation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics To update https://github.com/Ecogenomics/CheckM Metagenomics checkm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm 1.2.0 checkm-genome 1.2.2 (0/10) (0/10) (10/10) True True -cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri 0.7 cherri 0.8 (0/2) (0/2) (2/2) True False +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. 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 0.7 cherri 0.8 (0/2) (0/2) (2/2) True False chira 74.0 chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira 1.4.3 chira 1.4.3 (5/5) (0/5) (5/5) True False chromeister 2130.0 182.0 chromeister ultra-fast pairwise genome comparisons Up-to-date https://github.com/estebanpw/chromeister Sequence Analysis chromeister iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister 1.5.a chromeister 1.5.a (0/1) (1/1) (1/1) True False circexplorer2 269.0 16.0 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. RNA splicing, Gene transcripts, Literature and language Up-to-date https://github.com/YangLab/CIRCexplorer2 RNA, Assembly circexplorer2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 2.3.8 circexplorer2 2.3.8 (0/1) (0/1) (1/1) True False @@ -301,7 +302,7 @@ clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-perfor clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins " clustal2 " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) True True -codeml 60901.0 29.0 codeml Detects positive selection To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) True True +codeml 60901.0 29.0 codeml Detects positive selection 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 4.9 paml 4.10.7 (0/1) (0/1) (1/1) True True cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) True True colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) True False concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) True True @@ -315,9 +316,9 @@ das_tool 550.0 17.0 Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved m deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep learning Up-to-date https://github.com/BolognaBiocomp/deepsig Genome annotation deepsig iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig 1.2.5 deepsig 1.2.5 (0/1) (0/1) (1/1) True False deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis Transcriptomics To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) True False dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) True False -diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond 2.0.15 diamond 2.1.8 (3/3) (3/3) (3/3) True True +diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) True True disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. Protein sequence analysis Structure determination To update http://disco.omicsbio.org/ Metagenomics, Assembly disco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ disco 1.2 (1/1) (0/1) (1/1) True True -dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) True True +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 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 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) True True drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.4.5 (0/2) (0/2) (2/2) True True dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) True False edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) True False @@ -325,15 +326,15 @@ egsea 2524.0 177.0 egsea This tool implements the Ensemble of Gene Set Enrichmen emboss_5 89530.0 1816.0 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology To update http://emboss.open-bio.org/ Sequence Analysis, Fasta Manipulation emboss_5 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 5.0.0 emboss 6.6.0 (107/107) (107/107) (107/107) True False exomedepth 410.0 29.0 exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases To update https://cran.r-project.org/package=ExomeDepth Sequence Analysis, Variant Analysis exomedepth crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth 1.1.0 r-exomedepth 1.1.16 (1/1) (0/1) (1/1) True False exonerate 988.0 59.0 exonerate Exonerate is a generic tool for pairwise sequence comparison. exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Up-to-date https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Sequence Analysis exonerate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate 2.4.0 exonerate 2.4.0 (1/1) (1/1) (1/1) True False -export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn To update https://bitbucket.org/CibioCM/export2graphlan/overview Metagenomics export2graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) True True -fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) Up-to-date https://github.com/fannyhb/fargene Sequence Analysis fargene iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene 0.1 fargene 0.1 (1/1) (0/1) (1/1) True True +export2graphlan 5265.0 200.0 export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 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/ 0.20 export2graphlan 0.22 (1/1) (1/1) (1/1) True True +fargene 459.0 52.0 fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 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 0.1 fargene 0.1 (1/1) (0/1) (1/1) True True fasta_nucleotide_color_plot 322.0 39.0 fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. To update https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot Visualization fasta_nucleotide_color_plot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot 1.0.1 openjdk (1/1) (0/1) (1/1) True False fasta_stats 35332.0 1080.0 fasta-stats Display summary statistics for a fasta file. To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ Sequence Analysis fasta_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy (1/1) (1/1) (1/1) True False fastani 3498.0 250.0 fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity To update https://github.com/ParBLiSS/FastANI Sequence Analysis fastani iuc 1.3 fastani 1.34 (0/1) (0/1) (1/1) True False fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files " fastp " To update https://github.com/OpenGene/fastp Sequence Analysis fastp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp fastp 0.23.4 (1/1) (1/1) (1/1) True True -fastqe 4333.0 1266.0 fastqe FASTQE To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) True True +fastqe 4333.0 1266.0 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 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) True True fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) True True featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation Sequencing To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) True False feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) True False @@ -345,7 +346,7 @@ filtlong 30483.0 617.0 filtlong Filtlong - Filtering long reads by quality " flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. To update https://github.com/BrooksLabUCSC/flair Nanopore flair iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair 1.5 flair 2.0.0 (0/2) (0/2) (2/2) True False flash 13759.0 74.0 flash Fast Length Adjustment of SHort reads flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Up-to-date https://ccb.jhu.edu/software/FLASH/ Assembly, Fastq Manipulation flash iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash 1.2.11 flash 1.2.11 (1/1) (0/1) (1/1) True False fraggenescan 1102.0 68.0 fraggenescan Tool for finding (fragmented) genes in short read fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads Gene prediction Genetics, Sequence analysis To update https://sourceforge.net/projects/fraggenescan/ Sequence Analysis fraggenescan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ fraggenescan 1.31 (0/1) (1/1) (1/1) True True -freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.8 (2/4) (0/4) (4/4) True True +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation freyja To update https://github.com/andersen-lab/Freyja Metagenomics, Sequence Analysis freyja iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja 1.4.4 freyja 1.4.9 (2/4) (0/4) (4/4) True True funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. " funannotate " To update https://funannotate.readthedocs.io Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate 1.8.15 (3/5) (5/5) (5/5) True True @@ -356,32 +357,32 @@ genomic_super_signature 46.0 11.0 genomic_super_signature Interpretation of RNAs getorganelle 495.0 18.0 get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Up-to-date https://github.com/Kinggerm/GetOrganelle Assembly getorganelle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle 1.7.7.0 getorganelle 1.7.7.0 (0/2) (2/2) (2/2) True False gff3_rebase 110.0 12.0 gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase Sequence Analysis gff3_rebase iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 (1/1) (1/1) (1/1) True False gffread 10995.0 680.0 gffread gffread filters and/or converts GFF3/GTF2 records gffread gffread program for filtering, converting and manipulating GFF files Sequence annotation Nucleic acids, Sequence analysis Up-to-date http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ Sequence Analysis gffread devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread 0.12.7 gffread 0.12.7 (1/1) (1/1) (1/1) True False -ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base (5/5) (2/5) (5/5) True False +ggplot2 ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. Visualisation Data visualisation To update https://github.com/tidyverse/ggplot2 Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 3.4.0 r-base (5/5) (5/5) (5/5) True False glimmer glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based Glimmer makes gene predictions. gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. Sequence analysis, Genetic variation analysis Sequence analysis To update https://ccb.jhu.edu/software/glimmer/ Sequence Analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer glimmer 3.02 (0/8) (0/8) (4/8) True True goenrichment 5206.0 321.0 goenrichment, goslimmer Performs GO Enrichment analysis. goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. Gene-set enrichment analysis Transcriptomics Up-to-date https://github.com/DanFaria/GOEnrichment Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment 2.0.1 goenrichment 2.0.1 (2/2) (2/2) (2/2) True True goseq 19167.0 1210.0 goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. Gene functional annotation RNA-Seq To update https://bioconductor.org/packages/release/bioc/html/goseq.html Statistics, RNA, Micro-array Analysis goseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq 1.50.0 bioconductor-goseq 1.54.0 (1/1) (1/1) (1/1) True True -graphlan 5002.0 247.0 graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees To update https://bitbucket.org/nsegata/graphlan/overview Metagenomics, Graphics, Phylogenetics graphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ graphlan 1.1.3 (2/2) (2/2) (2/2) True True -gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) True True -gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.1 (1/1) (1/1) (1/1) True True +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 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/ graphlan 1.1.3 (2/2) (2/2) (2/2) True True +gtdbtk gtdbtk_classify_wf GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins To update https://github.com/Ecogenomics/GTDBTk Metagenomics gtdbtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk 2.2.2 gtdbtk 2.3.2 (0/1) (1/1) (0/1) True True +gubbins 3340.0 145.0 gubbins Gubbins - bacterial recombination detection gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing To update Sequence Analysis gubbins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins 3.2.1 gubbins 3.3.3 (1/1) (1/1) (1/1) True True gwastools gwastools_manhattan_plot gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. Deposition, Analysis, Annotation GWAS study To update https://bioconductor.org/packages/release/bioc/html/GWASTools.html Visualization, Variant Analysis iuc 0.1.0 bioconductor-gwastools 1.48.0 (0/1) (0/1) (0/1) True False -hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 (0/2) (0/2) (2/2) True True +hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. 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 To update https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization 1.0.3 hamronization 1.1.4 (0/2) (0/2) (2/2) True True hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) True True hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) True False -hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog 1.3.6 hapog 1.3.7 (0/1) (0/1) (1/1) True False +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes 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 1.3.7 hapog 1.3.7 (0/1) (0/1) (1/1) True False heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 3.1.3 r-gplots 2.17.0 (1/1) (1/1) (1/1) True False heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. bionet BioNet This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. Protein interaction analysis Molecular interactions, pathways and networks, Protein interactions To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) True False hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) True False hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff 3.1.5 hicstuff 3.2.1 (0/1) (0/1) (0/1) True False -hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) True True +hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 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 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) True True hisat2 299104.0 4183.0 hisat2 HISAT2 is a fast and sensitive spliced alignment program. hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Sequence alignment RNA-seq Up-to-date http://ccb.jhu.edu/software/hisat2/ Assembly hisat2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 2.2.1 hisat2 2.2.1 (1/1) (1/1) (1/1) True False hmmer3 21049.0 111.0 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families To update http://hmmer.org/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 3.3.2 hmmer 3.4 (0/12) (12/12) (12/12) True True homer homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Sequence motif discovery Up-to-date http://homer.ucsd.edu/homer/index.html Sequence Analysis data_manager_homer_preparse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer 4.11 homer 4.11 (0/5) (0/5) (5/5) True False -htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis To update https://readthedocs.org/projects/htseq/ Genomic Interval Operations, SAM, Sequence Analysis, RNA htseq_count lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count 0.9.1+galaxy1 htseq 2.0.5 (1/1) (1/1) (1/1) True False -humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (6/13) (13/13) True True +htseq_count 154533.0 1419.0 htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data Nucleic acid sequence analysis Sequence analysis 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 2.0.5 htseq 2.0.5 (1/1) (1/1) (1/1) True False +humann 5856.0 247.0 humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Up-to-date http://huttenhower.sph.harvard.edu/humann Metagenomics humann iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann 3.8 humann 3.8 (6/13) (10/13) (13/13) True True hybpiper hybpiper Analyse targeted sequence capture data HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Up-to-date https://github.com/mossmatters/HybPiper Sequence Analysis, Phylogenetics hybpiper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper 2.1.6 hybpiper 2.1.6 (0/1) (1/1) (0/1) True False hyphy hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary Hypothesis Testing using Phylogenies HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks To update http://www.hyphy.org Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ 2.5.47 hyphy 2.5.59 (17/17) (2/17) (17/17) True True hypo 354.0 39.0 hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Optimisation and refinement, Genome assembly Sequence assembly, Genomics Up-to-date https://github.com/kensung-lab/hypo Assembly hypo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo 1.0.3 hypo 1.0.3 (0/1) (0/1) (1/1) True True -icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.1 icescreen 1.3.1 (0/1) (0/1) (0/1) True True +icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Up-to-date https://icescreen.migale.inrae.fr/ Genome annotation icescreen iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.1 icescreen 1.3.1 (0/1) (0/1) (0/1) True True idba_ud 721.0 43.0 idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. Sequence assembly Sequence assembly To update https://i.cs.hku.hk/~alse/hkubrg/projects/index.html Assembly idba iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud idba 1.1.3 (3/3) (0/3) (3/3) True True idr 2873.0 30.0 idr Galaxy wrappers for the IDR package from Nathan Boleu To update https://github.com/nboley/idr Sequence Analysis idr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ 2.0.3 idr 2.0.4.2 (1/1) (0/1) (1/1) True False iedb_api 1506.0 12.0 iedb_api Get epitope binding predictions from IEDB-API To update http://tools.immuneepitope.org/main/tools-api/ Data Source, Sequence Analysis iedb_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api 2.15.2 python (0/1) (0/1) (1/1) True False @@ -394,19 +395,19 @@ isoformswitchanalyzer 822.0 29.0 isoformswitchanalyzer Statistical identificatio ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing Up-to-date https://github.com/andersen-lab/ivar Sequence Analysis ivar iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ 1.4.2 ivar 1.4.2 (5/5) (5/5) (5/5) True True jbrowse 18229.0 2346.0 jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. Genome visualisation Genomics Up-to-date https://jbrowse.org Sequence Analysis jbrowse iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse 1.16.11 jbrowse 1.16.11 (2/2) (2/2) (2/2) True True jcvi_gff_stats 2469.0 255.0 jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) To update https://github.com/tanghaibao/jcvi Sequence Analysis jcvi_gff_stats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats 0.8.4 jcvi 1.3.9 (1/1) (1/1) (1/1) True False -jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.0 (0/1) (1/1) (1/1) True True +jellyfish 1138.0 91.0 jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. k-mer counting Sequence analysis, Genomics To update https://github.com/gmarcais/Jellyfish Assembly jellyfish iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish kmer-jellyfish 2.3.1 (0/1) (1/1) (1/1) True True kc-align kc-align Kc-Align custom tool kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments Multiple sequence alignment Mapping Up-to-date https://github.com/davebx/kc-align Sequence Analysis kc_align iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align 1.0.2 kcalign 1.0.2 (1/1) (0/1) (1/1) True True khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. Standardisation and normalisation, De-novo assembly Sequence assembly Up-to-date https://khmer.readthedocs.org/ Assembly, Next Gen Mappers khmer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer 3.0.0a3 khmer 3.0.0a3 (8/8) (8/8) (8/8) True True kleborate 319.0 38.0 kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Up-to-date https://github.com/katholt/Kleborate/wiki Metagenomics kleborate iuc https://github.com/katholt/Kleborate 2.3.2 kleborate 2.3.2 (0/1) (0/1) (1/1) True True kofamscan 594.0 33.0 kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model Up-to-date https://github.com/takaram/kofam_scan Sequence Analysis kofamscan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan 1.3.0 kofamscan 1.3.0 (0/1) (0/1) (1/1) True True kraken_biom 1444.0 182.0 kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) Up-to-date https://github.com/smdabdoub/kraken-biom Metagenomics kraken_biom iuc https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 (0/1) (1/1) (1/1) True True kraken_taxonomy_report 2527.0 354.0 kraken_taxonomy_report Kraken taxonomy report To update https://github.com/blankenberg/Kraken-Taxonomy-Report Metagenomics kraken_taxonomy_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report 0.0.3 biopython 1.70 (1/1) (0/1) (1/1) True True -krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 (1/6) (2/6) (6/6) True True +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files Visualisation, Aggregation Taxonomy, Metagenomics Up-to-date https://github.com/jenniferlu717/KrakenTools Metagenomics krakentools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools 1.2 krakentools 1.2 (1/6) (4/6) (6/6) True True krocus krocus Predict MLST directly from uncorrected long reads To update https://github.com/quadram-institute-bioscience/krocus Sequence Analysis krocus iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus 1.0.1 krocus 1.0.3 (0/1) (0/1) (0/1) True True -last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last 1205 last 1526 (0/5) (0/5) (5/5) True False +last 227.0 41.0 last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. last LAST Short read alignment program incorporating quality scores Sequence alignment Genomics, Comparative genomics To update http://last.cbrc.jp/ Sequence Analysis last iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last 1205 last 1541 (0/5) (0/5) (5/5) True False legsta 55.0 7.0 legsta Performs in silico Legionella pneumophila sequence based typing. Up-to-date https://github.com/tseemann/legsta Sequence Analysis legsta iuc https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 (0/1) (0/1) (1/1) True True length_and_gc_content 4090.0 322.0 length_and_gc_content Gets gene length and gc content from a fasta and a GTF file To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content Fasta Manipulation, Statistics, RNA, Micro-array Analysis length_and_gc_content iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 (1/1) (1/1) (1/1) True False -limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics To update http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom 3.50.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) True False +limma_voom 20344.0 1012.0 limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics 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 3.58.1 bioconductor-limma 3.58.1 (1/1) (1/1) (1/1) True False lineagespot 37.0 2.0 lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation To update https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html Metagenomics, Sequence Analysis lineagespot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot 1.4.0 r-base (0/1) (0/1) (1/1) True True links 405.0 77.0 links Scaffold genome assemblies with long reads. links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Up-to-date https://github.com/bcgsc/LINKS Assembly links iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links 2.0.1 links 2.0.1 (0/1) (1/1) (1/1) True False lorikeet lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) Up-to-date https://github.com/AbeelLab/lorikeet Sequence Analysis lorikeet_spoligotype iuc https://github.com/AbeelLab/lorikeet 20 lorikeet 20 (0/1) (0/1) (1/1) True True @@ -422,7 +423,7 @@ mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs m medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning To update https://github.com/nanoporetech/medaka Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka 1.7.2 medaka 1.11.3 (3/4) (3/4) (3/4) True True megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) True True megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) True True -megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.24.20 (0/7) (0/7) (7/7) True True +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) True True meningotype meningotype Assign sequence type to N. meningitidis genome assemblies Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) True True merqury 2483.0 244.0 merqury Merqury is a tool for evaluating genomes assemblies based of k-mer operations. merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Up-to-date https://github.com/marbl/merqury Assembly merqury iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True meryl 6785.0 350.0 meryl Meryl a k-mer counter. meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Up-to-date https://github.com/marbl/meryl Assembly meryl iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl 1.3 merqury 1.3 (1/1) (1/1) (1/1) True True @@ -452,7 +453,7 @@ necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore re newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) True True nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) True True nonpareil 142.0 5.0 nonpareil Estimate average coverage in metagenomic datasets To update http://nonpareil.readthedocs.io Metagenomics nonpareil iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil 3.1.1 nonpareil 3.4.1 (1/1) (0/1) (1/1) True True -novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty 4.3.1 novoplasty 4.3.3 (0/1) (1/1) (1/1) True False +novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. To update https://github.com/ndierckx/NOVOPlasty Assembly novoplasty iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty 4.3.1 novoplasty 4.3.5 (0/1) (1/1) (1/1) True False nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. Up-to-date http://nugentechnologies.github.io/nudup/ SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) True True obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) True False odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.4 (0/2) (0/2) (2/2) True False @@ -468,9 +469,9 @@ pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriopha " To update https://github.com/gbouras13/pharokka Genome annotation pharokka iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka 1.3.2 " pharokka " (0/1) (1/1) (1/1) True True -phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3) True True +phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data 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 To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3) True True phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) True True -picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) True True +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 (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 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) True True picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) True True plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) True True plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) True True @@ -498,7 +499,7 @@ rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1) True False raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1) True True read_it_and_keep 3370.0 71.0 read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads To update https://github.com/GenomePathogenAnalysisService/read-it-and-keep Sequence Analysis read_it_and_keep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 (1/1) (0/1) (1/1) True True -recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Up-to-date https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.13.2 recentrifuge 1.13.2 (0/1) (0/1) (1/1) True True +recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing To update https://github.com/khyox/recentrifuge Metagenomics recentrifuge iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge 1.13.2 recentrifuge 1.14.0 (0/1) (0/1) (1/1) True True red 578.0 88.0 red Red (REpeat Detector) Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) True False repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) True False repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) True False @@ -519,7 +520,7 @@ scpipe 628.0 11.0 scpipe A flexible preprocessing pipeline for single-cell RNA-s semibin 183.0 10.0 semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Up-to-date https://semibin.readthedocs.io/en/latest/ Metagenomics semibin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin 2.0.2 semibin 2.0.2 (0/6) (0/6) (6/6) True True seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. Read mapping, Genetic variation analysis Transcriptomics, Mapping Up-to-date https://github.com/TRON-Bioinformatics/seq2HLA Sequence Analysis seq2hla iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla 2.3 seq2hla 2.3 (0/1) (0/1) (1/1) True False seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) True False -seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.6.1 (0/3) (0/3) (3/3) True True +seqkit seqkit_fx2tab, seqkit_locate, seqkit_stats A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit 2.3.1 seqkit 2.7.0 (0/3) (0/3) (3/3) True True seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 1.2.1 seqsero2 1.2.1 (0/1) (0/1) (1/1) False seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) True False seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ 0.7.5 seqwish 0.7.9 (0/1) (0/1) (1/1) True False @@ -561,23 +562,23 @@ tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformat tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) True False tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) True False transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) True False -transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 (5/5) (2/5) (5/5) True False +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ 3.0.2 transit 3.2.3 (5/5) (4/5) (5/5) True False transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes To update Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) True True -trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (11/13) (13/13) True False +trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity 2.15.1 trinity 2.15.1 (8/13) (12/13) (13/13) True False trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) True False trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler 0.5.4 trycycler 0.5.4 (0/5) (5/5) (5/5) True False tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. To update https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra 1.1.2 tsebra 1.1.2.2 (0/1) (0/1) (1/1) True False ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l 377 ucsc-blat 445 (0/1) (0/1) (0/1) True False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 (5/5) (3/5) (5/5) True False +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools 1.1.2 umi_tools 1.1.4 (5/5) (5/5) (5/5) True False unicycler 65732.0 1558.0 unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Up-to-date https://github.com/rrwick/Unicycler Assembly unicycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler 0.5.0 unicycler 0.5.0 (1/1) (1/1) (1/1) True True usher 1060.0 5.0 usher_matutils, usher UShER toolkit wrappers To update https://github.com/yatisht/usher Phylogenetics usher iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher 0.2.1 usher 0.6.3 (0/2) (0/2) (2/2) True True valet 637.0 20.0 valet A pipeline for detecting mis-assemblies in metagenomic assemblies. To update https://github.com/marbl/VALET Metagenomics valet iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet valet 1.0 (1/1) (0/1) (1/1) True True vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence data vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Up-to-date https://github.com/connor-lab/vapor Sequence Analysis vapor iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor 1.0.2 vapor 1.0.2 (1/1) (0/1) (1/1) True True -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP 1.1.1 varvamp 1.1.1 (0/1) (0/1) (0/1) False +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP 1.1.1 varvamp 1.1.1 (0/1) (0/1) (1/1) False vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) True True velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. Formatting, De-novo assembly Sequence assembly To update https://www.ebi.ac.uk/~zerbino/velvet/ Assembly velvet devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet velvet 1.2.10 (2/2) (2/2) (2/2) True True velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) True True -verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko 1.3.1 verkko 1.4.1 (0/1) (0/1) (1/1) True False +verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko 1.3.1 verkko 2.0 (0/1) (0/1) (1/1) True False vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg 1.23.0 vg 1.54.0 (0/3) (0/3) (3/3) True False volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) True False vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch 2.8.3 vsearch 2.27.0 (8/8) (8/8) (8/8) True True @@ -587,10 +588,10 @@ windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) True False bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) True True bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) True False -bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (0/4) (4/4) True False +bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split 2.5.2 bamtools 2.5.2 (4/4) (2/4) (4/4) True False biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) True True kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ kraken 1.1.1 (5/5) (5/5) (5/5) True True -kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) True True +kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. 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/ 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) True True ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.3 (0/1) (1/1) (1/1) True False bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) True False blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) True False @@ -659,7 +660,7 @@ proteomiqon_psmstatistics 694.0 4.0 proteomiqon_psmstatistics The PSMStatistics proteore_venn_diagram 15.0 proteore_venn_diagram ProteoRE JVenn Diagram To update Proteomics proteore_venn_diagram galaxyp 2021.06.08 python (0/1) (0/1) (0/1) True False psm_validation 20.0 psmvalidator Validate PSM from Ion Fragmentation To update https://github.com/galaxyproteomics/psm_fragments.git Proteomics psm_validation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation 1.0.3 (0/1) (0/1) (1/1) True False pyprophet pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. To update https://github.com/PyProphet/pyprophet Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 2.1.4 pyprophet 2.2.5 (0/6) (4/6) (6/6) True False -pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.6.3 (0/1) (0/1) (1/1) True False +pyteomics mztab2tsv Tools using the pyteomics library pyteomics Pyteomics Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. Protein identification Proteomics, Proteomics experiment To update https://pyteomics.readthedocs.io/en/latest/ Proteomics, Metabolomics pyteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics 4.4.1 pyteomics 4.7 (0/1) (0/1) (1/1) True False quantp 230.0 6.0 quantp Correlation between protein and transcript abundance To update Proteomics quantp galaxyp 1.1.2 r-data.table 1.11.6 (0/1) (0/1) (1/1) True False quantwiz_iq 32.0 1.0 quantwiz_iq Isobaric Quantitation using QuantWiz-IQ Up-to-date https://sourceforge.net/projects/quantwiz/ Proteomics quantwiz_iq galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq 2.0 quantwiz-iq 2.0 (0/1) (0/1) (1/1) True False rawtools 175.0 14.0 rawtools Raw Tools To update https://github.com/kevinkovalchik/RawTools Proteomics rawtools galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools rawtools 2.0.4 (0/1) (1/1) (1/1) True False @@ -676,12 +677,13 @@ blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs To update http://artbio.fr RNA, Sequence Analysis, Assembly blastx_to_scaffold artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 1.1.1 python (0/1) (0/1) (0/1) True False cap3 7766.0 101.0 cap3 cap3 wrapper To update http://artbio.fr Assembly cap3 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 2.0.1 cap3 10.2011 (0/1) (1/1) (1/1) True False deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 (0/1) (0/1) (0/1) True False +ez_histograms ez_histograms ggplot2 histograms and density plots To update https://github.com/tidyverse/ggplot2 Visualization, Statistics ez_histograms artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms 3.4.4 r-ggplot2 2.2.1 (0/1) (0/1) (0/1) False fisher_test fishertest Fisher's exact test on two-column hit lists. To update http://artbio.fr RNA, Statistics fishertest artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 (0/1) (0/1) (0/1) True False gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization 4.3+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) True False guppy guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies To update http://artbio.fr Nanopore guppy_basecaller artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0.2.2 (0/1) (0/1) (0/1) True False high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps To update https://github.com/cran/gplots Visualization high_dim_heatmap artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap 3.1.3+galaxy0 r-gplots 2.17.0 (0/1) (0/1) (0/1) True False -mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats 0.19.1+galaxy0 r-optparse 1.3.2 (0/1) (0/1) (0/1) True False -mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.5.1 tar (0/1) (1/1) (0/1) True False +mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 (0/1) (0/1) (0/1) True False +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.6 tar (0/1) (1/1) (0/1) True False oases oasesoptimiserv Short read assembler To update http://artbio.fr Assembly, RNA oases artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/oases 1.3.0 oases 0.2.09 (0/1) (0/1) (0/1) True False probecoverage probecoverage computes and plots read coverage of genomic regions by sequencing datasets To update http://artbio.fr Sequence Analysis, Genomic Interval Operations, Graphics, Statistics probecoverage artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage 0.7.0 samtools 1.19.2 (0/1) (0/1) (0/1) True False rsem 2273.0 199.0 extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem rsem 1.3.3 (0/4) (0/4) (1/4) True False