From 4b6ba67f5c9fa46756c1b7f022d5063391b0cc42 Mon Sep 17 00:00:00 2001 From: github-actions Date: Sun, 7 Apr 2024 11:43:01 +0000 Subject: [PATCH] fetch all tools bot - step fetch --- results/repositories03.list_tools.tsv | 48 +++++++++++++-------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/results/repositories03.list_tools.tsv b/results/repositories03.list_tools.tsv index fbbfa32a..5c47b79b 100644 --- a/results/repositories03.list_tools.tsv +++ b/results/repositories03.list_tools.tsv @@ -51,7 +51,7 @@ blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GF bowtie2 380252.0 5136.0 bowtie2 Bowtie2: Fast and sensitive read alignment bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Read mapping Mapping, Genomics, Mapping Up-to-date http://bowtie-bio.sourceforge.net/bowtie2 Next Gen Mappers bowtie2 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 2.5.3 bowtie2 2.5.3 (1/1) (1/1) (1/1) (1/1) bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (0/1) (0/1) (1/1) (1/1) breseq 1871.0 50.0 breseq Predicts mutations in microbial genomes breseq breseq breseq Runs Breseq software on a set of fastq files. Polymorphism detection Sequencing, Sequence analysis, DNA mutation To update https://github.com/barricklab/breseq Variant Analysis breseq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq 0.35.5 breseq 0.38.3 (0/1) (1/1) (1/1) (0/1) -busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.0 (1/1) (1/1) (1/1) (1/1) +busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) bwa 957912.0 5279.0 bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Up-to-date http://bio-bwa.sourceforge.net/ Next Gen Mappers bwa devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa 0.7.17 bwa 0.7.17 (2/2) (2/2) (2/2) (2/2) bwa_mem2 44386.0 1220.0 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Sequence alignment Mapping Up-to-date https://github.com/bwa-mem2/bwa-mem2 Next Gen Mappers bwa_mem2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 2.2.1 bwa-mem2 2.2.1 (1/1) (1/1) (1/1) (1/1) bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) @@ -77,9 +77,9 @@ cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file t cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit 0.9.10 cnvkit 0.9.10 (0/17) (0/17) (17/17) (0/17) codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) -colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (0/2) (0/2) (0/2) (0/2) +colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) -collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils (1/1) (1/1) (1/1) (1/1) +collection_column_join 20857.0 1483.0 collection_column_join Column Join on Collections To update Text Manipulation collection_column_join iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 0.0.3 coreutils 8.25 (1/1) (1/1) (1/1) (1/1) collection_element_identifiers 5059.0 912.0 collection_element_identifiers Extract element identifiers of a collection To update Text Manipulation collection_element_identifiers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.2 (1/1) (1/1) (1/1) (1/1) column_maker 3882097.0 2379.0 Add_a_column1 Compute an expression on every row To update Text Manipulation column_maker devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 2.0 python (1/1) (1/1) (1/1) (1/1) column_order_header_sort 3258.0 80.0 column_order_header_sort Sort Column Order by heading To update Text Manipulation column_order_header_sort iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 0.0.1 python (1/1) (0/1) (1/1) (1/1) @@ -87,13 +87,13 @@ column_remove_by_header 8424.0 199.0 column_remove_by_header Remove columns by h compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) compose_text_param 35084.0 375.0 compose_text_param Compose a text parameter value using text, integer and float values To update Text Manipulation compose_text_param iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 0.1.1 (1/1) (1/1) (1/1) (1/1) compress_file 3674.0 164.0 compress_file Compress files. To update Text Manipulation compress_file iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 0.1.0 gzip (1/1) (1/1) (1/1) (0/1) -concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics To update https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct (0/5) (0/5) (5/5) (5/5) +concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file To update https://github.com/galaxyproject/tools-iuc Sequence Analysis coverage_report iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0.0.4 perl-number-format 1.76 (0/1) (0/1) (0/1) (0/1) coverm coverm_contig, coverm_genome CoverM genome and contig wrappers coverm coverm CoverM Read coverage calculator for metagenomics Local alignment Bioinformatics Up-to-date https://github.com/wwood/CoverM Sequence Analysis coverm iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm 0.7.0 coverm 0.7.0 (0/2) (0/2) (2/2) (2/2) -crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio (0/1) (0/1) (1/1) (0/1) +crispr_studio 636.0 30.0 crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. crisprstudio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. Visualisation Sequence analysis, Genomics, Data visualisation To update https://github.com/moineaulab/CRISPRStudio Sequence Analysis crispr_studio iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio 1+galaxy0 crispr_studio 1 (0/1) (0/1) (1/1) (0/1) crosscontamination_barcode_filter 347.0 17.0 crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 (1/1) (0/1) (1/1) (0/1) crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies To update http://crossmap.sourceforge.net/ Convert Formats, Genomic Interval Operations crossmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 0.6.1 crossmap 0.7.0 (5/7) (0/7) (6/7) (0/7) -cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.7 cutadapt 4.7 (1/1) (1/1) (1/1) (1/1) +cutadapt 232004.0 5090.0 cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Up-to-date https://cutadapt.readthedocs.org/en/stable/ Fasta Manipulation, Fastq Manipulation, Sequence Analysis cutadapt lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt 4.7 cutadapt 4.7 (1/1) (1/1) (1/1) (1/1) cutesv 235.0 17.0 cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science To update https://github.com/tjiangHIT/cuteSV Variant Analysis cutesv iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv 1.0.8 cutesv 2.1.0 (0/1) (1/1) (1/1) (0/1) cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. To update ChIP-seq cwpair2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1.1.1 matplotlib (1/1) (0/1) (0/1) (0/1) dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics To update https://benjjneb.github.io/dada2/index.html Metagenomics dada2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 bioconductor-dada2 1.30.0 (10/10) (10/10) (10/10) (10/10) @@ -106,8 +106,8 @@ deepsig 5.0 deepsig Predictor of signal peptides in proteins based on deep lear deepvariant 1889.0 182.0 deepvariant DeepVariant is a deep learning-based variant caller To update https://github.com/google/deepvariant Variant Analysis deepvariant iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1.5.0 (1/1) (0/1) (1/1) (0/1) deg_annotate 19910.0 1774.0 deg_annotate Annotate DESeq2/DEXSeq output tables To update Transcriptomics deg_annotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 (1/1) (1/1) (1/1) (1/1) delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. delly2 delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases To update https://github.com/dellytools/delly Variant Analysis delly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly 0.9.1 delly 1.2.6 (0/6) (0/6) (6/6) (0/6) -deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis 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 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) -dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 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 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.44 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) +deseq2 95752.0 4990.0 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 (1/1) (1/1) (1/1) (1/1) +dexseq 16064.0 218.0 dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 (3/3) (3/3) (3/3) (3/3) diamond 49711.0 963.0 bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. Sequence alignment analysis Sequence analysis, Proteins To update https://github.com/bbuchfink/diamond Sequence Analysis diamond bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond 2.0.15 diamond 2.1.9 (3/3) (3/3) (3/3) (3/3) diffbind 6264.0 250.0 diffbind Diffbind provides functions for processing ChIP-Seq data. diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. Differential binding analysis ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/DiffBind.html ChIP-seq diffbind bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind 2.10.0 bioconductor-diffbind 3.12.0 (1/1) (1/1) (1/1) (1/1) dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. Up-to-date https://github.com/cbib/DIMet Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0.2.4 dimet 0.2.4 (0/1) (0/1) (0/1) (0/1) @@ -137,7 +137,7 @@ fastp 1055760.0 2803.0 fastp Fast all-in-one preprocessing for FASTQ files fastp fastqc 1556625.0 17447.0 fastqc Read QC reports using FastQC fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastq Manipulation fastqc devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc 0.74+galaxy0 fastqc 0.12.1 (1/1) (1/1) (1/1) (1/1) fastqe 4333.0 1266.0 fastqe FASTQE fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. Sequencing quality control Sequence analysis, Sequencing To update https://fastqe.com/ Sequence Analysis fastqe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe 0.3.1+galaxy0 fastqe 0.3.1 (1/1) (1/1) (1/1) (1/1) fasttree 55434.0 379.0 fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis To update http://www.microbesonline.org/fasttree/ Phylogenetics fasttree iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree 2.1.10 fasttree 2.1.11 (1/1) (1/1) (1/1) (1/1) -featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation 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 https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) +featurecounts 696399.0 4679.0 featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 (1/1) (1/1) (1/1) (1/1) feelnc 1191.0 46.0 feelnc Galaxy wrapper for FEELnc feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA To update https://github.com/tderrien/FEELnc Sequence Analysis feelnc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc 0.2.1 feelnc 0.2 (1/1) (0/1) (1/1) (1/1) fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. Up-to-date https://github.com/lh3/fermikit Assembly, Variant Analysis fermikit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit r193 fermi2 r193 (0/2) (0/2) (0/2) (0/2) fgsea 5240.0 307.0 fgsea Perform gene set testing using fgsea fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 (1/1) (1/1) (1/1) (1/1) @@ -183,10 +183,10 @@ gwastools gwastools_manhattan_plot gwastools gwastools GWASTools Classes for hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure Data handling, Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Up-to-date https://github.com/pha4ge/hAMRonization Sequence Analysis hamronization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization 1.1.4 hamronization 1.1.4 (0/2) (0/2) (2/2) (2/2) hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation Biohansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Up-to-date https://github.com/phac-nml/bio_hansel Sequence Analysis bio_hansel iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel 2.6.1 bio_hansel 2.6.1 (1/1) (0/1) (1/1) (0/1) hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" Haplotype mapping, Variant classification Up-to-date https://github.com/vibansal/HapCUT2 Assembly hapcut2 galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 1.3.3 hapcut2 1.3.3 (0/1) (1/1) (0/1) (0/1) -hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics To update https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.7 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) +hapog 295.0 36.0 hapog Hapo-G - Haplotype-Aware Polishing of Genomes hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. Genome assembly, Optimisation and refinement Sequence assembly, Genomics Up-to-date https://github.com/institut-de-genomique/HAPO-G Assembly hapog iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog 1.3.8 hapog 1.3.8 (0/1) (0/1) (1/1) (1/1) happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. hap.py hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism To update https://github.com/Illumina/hap.py Variant Analysis happy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy 0.3.14 hap.py 0.3.15 (0/1) (0/1) (0/1) (0/1) heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package To update https://github.com/cran/gplots Visualization ggplot2_heatmap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 3.1.3.1 r-gplots 2.17.0 (1/1) (1/1) (1/1) (1/1) -heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) +heinz 1186.0 242.0 heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz bionet, heinz Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 (4/4) (4/4) (4/4) (0/4) hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. To update https://github.com/deeptools/HiCExplorer Sequence Analysis, Visualization hicexplorer bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 3.7.2 hicexplorer 3.7.3 (0/40) (5/40) (40/40) (4/40) hicstuff hicstuff_pipeline To update https://github.com/koszullab/hicstuff Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 3.1.5 hicstuff 3.2.2 (0/1) (0/1) (0/1) (0/1) hifiasm_meta 137.0 12.0 hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. hifiasm-meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. Sequence assembly Sequence assembly, Metagenomics To update https://github.com/xfengnefx/hifiasm-meta Metagenomics hifiasm_meta galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta 0.3.1 hifiasm_meta hamtv0.3.1 (0/1) (1/1) (1/1) (0/1) @@ -263,7 +263,7 @@ medaka medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant megahit 9530.0 548.0 megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Up-to-date https://github.com/voutcn/megahit Sequence Analysis, Assembly, Metagenomics megahit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit 1.2.9 megahit 1.2.9 (1/1) (1/1) (1/1) (1/1) megahit_contig2fastg 475.0 54.0 megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly To update https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp Sequence Analysis, Assembly, Metagenomics megahit_contig2fastg iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg 1.1.3 megahit 1.2.9 (1/1) (0/1) (1/1) (0/1) megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. Sequence analysis, Taxonomic classification Sequence analysis To update https://github.com/husonlab/megan-ce Sequence Analysis megan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan 6.21.7 megan 6.25.9 (0/7) (0/7) (7/7) (0/7) -meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_fimo, meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) (0/4) +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. meme_meme meme_meme, meme_fimo meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability To update http://meme-suite.org/ ChIP-seq meme iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme 5.4.1 meme 5.5.5 (3/4) (0/4) (4/4) (0/4) meme_chip 6584.0 287.0 meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. To update http://meme-suite.org/ ChIP-seq meme_chip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 4.11.2 graphicsmagick 1.3.26 (1/1) (0/1) (1/1) (0/1) meningotype meningotype Assign sequence type to N. meningitidis genome assemblies meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. Genotyping, Multilocus sequence typing Microbiology, Genotype and phenotype Up-to-date https://github.com/MDU-PHL/meningotype Sequence Analysis meningotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype 0.8.5 meningotype 0.8.5 (0/1) (0/1) (0/1) (0/1) merlin merlin Pedigree Analysis package merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation Haplotype mapping, Genetic mapping GWAS study, Mapping Up-to-date http://csg.sph.umich.edu/abecasis/Merlin/ Variant Analysis merlin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin 1.1.2 merlin 1.1.2 (0/1) (0/1) (0/1) (0/1) @@ -276,7 +276,7 @@ metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) -minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping To update https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.27 minimap2 2.28 (1/1) (1/1) (1/1) (1/1) +minimap2 260442.0 1588.0 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences Pairwise sequence alignment Mapping Up-to-date https://github.com/lh3/minimap2 Next Gen Mappers minimap2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 2.28 minimap2 2.28 (1/1) (1/1) (1/1) (1/1) miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) @@ -289,7 +289,7 @@ mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mot msaboot 803.0 34.0 msaboot A multiple sequences alignment bootstrapping tool. Up-to-date https://github.com/phac-nml/msaboot Fasta Manipulation msaboot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 0.1.2 msaboot 0.1.2 (1/1) (0/1) (1/1) (0/1) multigps multigps Analyzes collections of multi-condition ChIP-seq data. To update http://mahonylab.org/software/multigps/ ChIP-seq multigps iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 0.74.0 fonts-conda-ecosystem (1/1) (0/1) (0/1) (0/1) multigsea 53.0 2.0 multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 (0/1) (0/1) (1/1) (0/1) -multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation Sequencing, Bioinformatics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.21 (1/1) (1/1) (1/1) (1/1) +multiqc 162790.0 8320.0 multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Validation, Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics To update http://multiqc.info/ Fastq Manipulation, Statistics, Visualization multiqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc 1.11 multiqc 1.21 (1/1) (1/1) (1/1) (1/1) mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools mummer4 mummer4 Up-to-date https://github.com/mummer4/mummer Sequence Analysis mummer4 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 4.0.0rc1 mummer4 4.0.0rc1 (6/6) (6/6) (6/6) (6/6) mykrobe mykrobe_predict Antibiotic resistance predictions Mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics To update https://github.com/Mykrobe-tools/mykrobe Sequence Analysis mykrobe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe 0.10.0 mykrobe 0.13.0 (0/1) (0/1) (0/1) (0/1) mzmine mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Up-to-date http://mzmine.github.io/ Metabolomics mzmine_batch iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine 3.9.0 mzmine 3.9.0 (0/1) (0/1) (1/1) (0/1) @@ -321,7 +321,7 @@ optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-dat orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection To update Data Source packaged_annotation_loader iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0.1 python (0/1) (0/1) (0/1) (0/1) -pairtools pairtools_parse Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.0.3 pairtools 1.0.3 (0/1) (0/1) (0/1) (0/1) +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.0.3 pairtools 1.0.3 (0/5) (0/5) (0/5) (0/5) pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) @@ -336,7 +336,7 @@ pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriopha " (0/1) (1/1) (1/1) (0/1) phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Up-to-date https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq 1.46.0 bioconductor-phyloseq 1.46.0 (0/4) (0/4) (4/4) (0/4) phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1) (1/1) -picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_fastqtosam, picard_samtofastq, picard_reordersam, picard_replacesamheader picard_samtofastq Create a FASTQ file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31) (31/31) +picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_samtofastq picard_samtofastq, picard_fastqtosam, picard_replacesamheader, picard_reordersam picard_samtofastq Create a FASTQ file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31) (31/31) pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (1/1) (1/1) (0/1) picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6) (6/6) picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) @@ -361,7 +361,7 @@ psiclass 15.0 1.0 psiclass PsiCLASS is a reference-based transcriptome assembler pureclip 1423.0 36.0 pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data To update https://github.com/skrakau/PureCLIP Sequence Analysis, RNA, CLIP-seq pureclip iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 1.0.4 pureclip 1.3.1 (0/1) (0/1) (1/1) (0/1) purge_dups 16800.0 167.0 purge_dups Purge haplotigs and overlaps in an assembly based on read depth purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences Genome assembly, Read binning, Scaffolding Sequence assembly Up-to-date https://github.com/dfguan/purge_dups Assembly purge_dups iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups 1.2.6 purge_dups 1.2.6 (1/1) (1/1) (1/1) (0/1) pycoqc 21123.0 350.0 pycoqc QC metrics for ONT Basecalling pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Up-to-date https://github.com/tleonardi/pycoQC Nanopore pycoqc iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc 2.5.2 pycoqc 2.5.2 (1/1) (1/1) (1/1) (1/1) -pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.1.0 (1/1) (0/1) (1/1) (0/1) +pyega3 pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. To update https://github.com/EGA-archive/ega-download-client Data Source ega_download_client iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 5.0.2 pyega3 5.2.0 (1/1) (0/1) (1/1) (0/1) pygenometracks 11332.0 377.0 pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. Visualisation, Formatting Model organisms, Imaging, Workflows Up-to-date https://github.com/deeptools/pyGenomeTracks Visualization pygenometracks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks 3.8 pygenometracks 3.8 (1/1) (1/1) (1/1) (1/1) pysradb pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics To update https://github.com/saketkc/pysradb Sequence Analysis pysradb_search iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb 1.4.2 pysradb 2.2.0 (0/1) (0/1) (1/1) (0/1) qfilt qfilt Filter sequencing data To update https://github.com/veg/qfilt Fastq Manipulation qfilt iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 1.0.0+galaxy1 qfilt 0.0.1 (0/1) (0/1) (0/1) (0/1) @@ -404,7 +404,7 @@ rseqc 135036.0 3269.0 rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_satu ruvseq 1236.0 76.0 ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 (1/1) (0/1) (1/1) (0/1) salsa2 salsa A tool to scaffold long read assemblies with Hi-C SALSA SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Up-to-date https://github.com/marbl/SALSA Assembly salsa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 2.3 salsa2 2.3 (1/1) (1/1) (1/1) (0/1) samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. Split read mapping DNA, Sequencing, Mapping To update https://github.com/GregoryFaust/samblaster SAM, Fastq Manipulation, Variant Analysis samblaster iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster 0.1.24 samblaster 0.1.26 (0/1) (0/1) (0/1) (0/1) -sansa sansa_annotate Sansa is a tool for structural variant annotation. To update https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.0.8 sansa 0.2.1 (0/1) (0/1) (1/1) (0/1) +sansa sansa_annotate Sansa is a tool for structural variant annotation. Up-to-date https://github.com/dellytools/sansa Variant Analysis sansa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0.2.1 sansa 0.2.1 (0/1) (0/1) (1/1) (0/1) sarscov2formatter 173.0 7.0 sarscov2formatter sarscov2formatter custom script Up-to-date https://github.com/nickeener/sarscov2formatter Sequence Analysis sarscov2formatter iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1.0 sarscov2formatter 1.0 (1/1) (0/1) (1/1) (0/1) sarscov2summary 140.0 1.0 sarscov2summary sarscov2summary custom script To update https://github.com/nickeener/sarscov2summary Sequence Analysis sarscov2summary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary 0.1 sarscov2summary 0.5 (1/1) (0/1) (1/1) (0/1) sbml2sbol sbml2sbol Convert SBML to SBOL format To update https://github.com/neilswainston/SbmlToSbol Synthetic Biology sbml2sbol iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol 0.1.13 sbml2sbol (0/1) (0/1) (0/1) (0/1) @@ -422,7 +422,7 @@ seq2hla 288.0 16.0 seq2hla Precision HLA typing and expression from RNAseq data seqcomplexity 68.0 16.0 seqcomplexity Sequence complexity for raw reads Up-to-date https://github.com/stevenweaver/seqcomplexity Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 0.1.2 seqcomplexity 0.1.2 (1/1) (0/1) (1/1) (0/1) seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. DNA transcription, Sequence trimming, DNA translation, Sequence conversion Database management, Sequence analysis To update https://bioinf.shenwei.me/seqkit/ Sequence Analysis seqkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit 2.3.1 seqkit 2.8.0 (0/5) (2/5) (3/5) (2/5) seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Up-to-date https://github.com/jstjohn/SeqPrep Fastq Manipulation, Sequence Analysis seqprep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep 1.3.2 seqprep 1.3.2 (0/1) (0/1) (1/1) (0/1) -seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Up-to-date https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.2.1 seqsero2 1.2.1 (0/1) (0/1) (1/1) (0/1) +seqsero2 12.0 seqsero2 Salmonella serotype prediction from genome sequencing data seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics To update https://github.com/denglab/SeqSero2 Sequence Analysis seqsero2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 1.2.1 seqsero2 1.3.1 (0/1) (0/1) (1/1) (0/1) seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Data handling, Sequence file editing Data management Up-to-date https://github.com/lh3/seqtk Sequence Analysis seqtk iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk 1.4 seqtk 1.4 (15/15) (15/15) (15/15) (15/15) seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.9 (0/1) (0/1) (1/1) (0/1) seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) @@ -447,11 +447,11 @@ snpeff-covid19 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic va snpfreqplot 3530.0 156.0 snpfreqplot Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ Variant Analysis snpfreqplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1.0 r-base (1/1) (1/1) (1/1) (1/1) socru 621.0 13.0 socru Order and orientation of complete bacterial genomes To update https://github.com/quadram-institute-bioscience/socru Sequence Analysis socru iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 2.1.7 socru 2.2.4 (1/1) (0/1) (1/1) (0/1) sonneityping 1.0 1.0 sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Up-to-date https://github.com/katholt/sonneityping Sequence Analysis sonneityping iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping 20210201 sonneityping 20210201 (0/1) (0/1) (1/1) (0/1) -spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades plasmidspades, rnaspades, spades, coronaspades, metaspades, metaviralspades, biosyntheticspades, metaplasmidspades, rnaviralspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) +spades 58834.0 2309.0 spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. spades rnaviralspades, coronaspades, metaspades, plasmidspades, rnaspades, metaviralspades, spades, metaplasmidspades, biosyntheticspades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. Genome assembly Sequence assembly Up-to-date https://github.com/ablab/spades Assembly, RNA, Metagenomics spades iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades 3.15.5 spades 3.15.5 (9/9) (9/9) (9/9) (9/9) spaln 446.0 34.0 list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. To update http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ Sequence Analysis, Genome annotation spaln iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2.4.9 python (2/2) (0/2) (2/2) (0/2) spotyping 1278.0 12.0 spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Up-to-date https://github.com/xiaeryu/SpoTyping-v2.0 Sequence Analysis spotyping iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping 2.1 spotyping 2.1 (0/1) (0/1) (1/1) (0/1) spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) -sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing To update https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.0.10 sra-tools 3.1.0 (3/3) (3/3) (3/3) (3/3) +sra-tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Data handling DNA, Genomics, Sequencing Up-to-date https://github.com/ncbi/sra-tools Data Source, Fastq Manipulation sra_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools 3.1.0 sra-tools 3.1.0 (3/3) (3/3) (3/3) (3/3) srst2 205.0 22.0 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens Multilocus sequence typing Whole genome sequencing, Public health and epidemiology To update http://katholt.github.io/srst2/ Metagenomics srst2 iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 0.2.0 samtools 1.19.2 (0/1) (0/1) (1/1) (0/1) stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. Data handling Mapping, Population genetics To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis stacks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks 2.65 (0/13) (13/13) (13/13) (12/13) stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq To update http://catchenlab.life.illinois.edu/stacks/ Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 2.55 stacks 2.65 (0/12) (12/12) (12/12) (12/12) @@ -477,7 +477,7 @@ telescope telescope_assign Single locus resolution of Transposable ELEment exp tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. Up-to-date http://hammelllab.labsites.cshl.edu/software/ Sequence Analysis tetoolkit iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 2.2.3 tetranscripts 2.2.3 (0/1) (1/1) (1/1) (0/1) tetyper 69.0 8.0 tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. Up-to-date https://github.com/aesheppard/TETyper Sequence Analysis tetyper iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1.1 tetyper 1.1 (1/1) (0/1) (1/1) (0/1) tn93 113.0 7.0 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences To update https://github.com/veg/tn93/ Sequence Analysis tn93 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 1.0.6 tn93 1.0.13 (4/4) (0/4) (4/4) (0/4) -tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.3 tracegroomer 0.1.3 (0/1) (0/1) (0/1) (0/1) +tracegroomer tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. Up-to-date https://github.com/cbib/TraceGroomer Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0.1.3 tracegroomer 0.1.3 (0/1) (0/1) (0/1) (1/1) tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0.6.1 tracy 0.7.6 (0/4) (0/4) (4/4) (0/4) transdecoder 5468.0 348.0 transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 (1/1) (1/1) (1/1) (1/1) transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. Transposon prediction DNA, Sequencing, Mobile genetic elements To update https://github.com/mad-lab/transit/ Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit 3.0.2 transit 3.2.3 (5/5) (5/5) (5/5) (0/5) @@ -485,7 +485,7 @@ transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminator trimmomatic 305866.0 5862.0 trimmomatic A flexible read trimming tool for Illumina NGS data Up-to-date http://www.usadellab.org/cms/?page=trimmomatic Fastq Manipulation trimmomatic pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 0.39 trimmomatic 0.39 (1/1) (1/1) (1/1) (1/1) trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) -trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers To update https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.4 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.4 (0/1) (0/1) (1/1) (1/1) tsne 368.0 10.0 tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation To update https://cran.r-project.org/web/packages/Rtsne/ Text Manipulation tsne iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 0.0.2 r-rtsne 0.13 (1/1) (0/1) (1/1) (1/1) tximport 1408.0 88.0 tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows To update http://bioconductor.org/packages/tximport/ Transcriptomics tximport iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.22.0 bioconductor-tximport 1.30.0 (1/1) (0/1) (1/1) (0/1) @@ -502,7 +502,7 @@ vapor 3164.0 94.0 vapor Classify Influenza samples from raw short read sequence vardict vardict_java VarDict - calls SNVs and indels for tumour-normal pairs To update https://github.com/AstraZeneca-NGS/VarDictJava Variant Analysis vardict_java iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 1.8.3 python (0/1) (0/1) (1/1) (0/1) variant_analyzer 88.0 3.0 mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data To update Variant Analysis variant_analyzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 2.0.0 matplotlib (3/3) (0/3) (3/3) (0/3) varscan 208.0 16.0 varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data To update https://dkoboldt.github.io/varscan/ Variant Analysis varscan iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 2.4.3 varscan 2.4.6 (3/3) (3/3) (3/3) (3/3) -varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.1.1 varvamp 1.1.1 (0/1) (0/1) (1/1) (0/1) +varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. PCR primer design Virology Up-to-date https://github.com/jonas-fuchs/varVAMP/ Sequence Analysis varvamp iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp 1.1.2 varvamp 1.1.2 (0/1) (0/1) (1/1) (0/1) vcf2maf 751.0 29.0 vcf2maf vcf2maf: Convert VCF into MAF Up-to-date Convert Formats vcf2maf iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 1.6.21 vcf2maf 1.6.21 (0/1) (1/1) (1/1) (0/1) vcfanno 872.0 87.0 vcfanno Annotate VCF files vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. SNP annotation Genetic variation, Data submission, annotation and curation Up-to-date https://github.com/brentp/vcfanno Variant Analysis vcfanno iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno 0.3.5 vcfanno 0.3.5 (0/1) (0/1) (1/1) (0/1) vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science To update https://cran.r-project.org/package=vegan Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan 2.4-3 r-vegan 2.3_4 (3/3) (0/3) (3/3) (0/3)