From f72d09a55997da3db1887294d0c780329a12a27d Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 7 Nov 2024 16:30:15 +0100 Subject: [PATCH] multiple tools --- .../microgalaxy/lab/sections/5_tools.yml | 752 +----------------- 1 file changed, 11 insertions(+), 741 deletions(-) diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 77e11abf..11a75ac8 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -1,744 +1,14 @@ id: tools +title: Community Tools tabs: -- content: - - description_md: Tools to compute and analyse biodiversity metrics - title_md: PAMPA - - description_md: TreeBeST best - title_md: TreeBest - - description_md: Order and Orientate Contigs - title_md: abacas - - description_md: Mass screening of contigs for antiobiotic resistance genes - title_md: abricate - - description_md: A pipeline for running AMRfinderPlus and collating results into - functional classes - title_md: abritamr - - description_md: Assembly By Short Sequences - a de novo, parallel, paired-end - sequence assembler - title_md: abyss - - description_md: Performs analysis Of differential abundance taking sample variation - into account - title_md: aldex2 - - description_md: AmpliCan is an analysis tool for genome editing. - title_md: amplican - - description_md: '"AMRFinderPlus is designed to find acquired antimicrobial resistance - genes and point mutations in protein and/or assembled nucleotide sequences.It - can also search "plus", stress, heat, and biocide resistance and virulence factors - for some organisms.' - title_md: amrfinderplus - - description_md: Performs analysis of compositions of microbiomes with bias correction. - title_md: ancombc - - description_md: Antismash allows the genome-wide identification, annotation and - analysis of secondary metabolite biosynthesis gene clusters - title_md: antismash - - description_md: 'The artic pipeline is designed to help run the artic bioinformatics - protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: - read filtering, primer trimming, amplicon coverage normalisation,variant calling - and consensus building' - title_md: artic - - description_md: Summarise an assembly (e.g. N50 metrics) - title_md: assemblystats - - description_md: '"Bakta is a tool for the rapid & standardized annotation of bacterial - genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and - sORF-including annotations in machine-readable JSON & bioinformatics standard - file formats for automatic downstream analysis."' - title_md: bakta - - description_md: Operate on and transform BAM datasets in various ways using bamtools - title_md: bamtools - - description_md: Bandage - A Bioinformatics Application for Navigating De novo - Assembly Graphs Easily - title_md: bandage - - description_md: Detecting natural selection from population-based genetic data - title_md: bayescan - - description_md: BBTools is a suite of fast, multithreaded bioinformatics tools - designed for analysis of DNA and RNA sequence data.BBTools can handle common - sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed - or raw,with autodetection of quality encoding and interleaving. It is written - in Java and works on any platform supportingJava, including Linux, MacOS, and - Microsoft Windows and Linux; there are no dependencies other than Java (version7 - or higher). Program descriptions and options are shown when running the shell - scripts with no parameters. - title_md: bbtools - - description_md: Construct sequence similarity networks of BGCs and groups them - into GCF - title_md: bigscape - - description_md: Reconciles the outputs of different binning programs with the - aim to improve the quality of genome bins,especially with respect to contamination - levels. - title_md: binning_refiner - - description_md: Heidelberg and Enteritidis SNP Elucidation - title_md: biohansel - - description_md: The biom-format package provides a command line interface and - Python API for working with BIOM files. - title_md: biom_format - - description_md: Bio-Tradis is a tool suite dedicated to essentiality analyses - with TraDis data. - title_md: biotradis - - description_md: Maps BLAST results to GO annotation terms - title_md: blast2go - - description_md: BLAST Reciprocal Best Hits (RBH) from two FASTA files - title_md: blast_rbh - - description_md: Make table of top BLAST match descriptions - title_md: blastxml_to_top_descr - - description_md: Bayesian Reestimation of Abundance with KrakEN - title_md: bracken - - description_md: BUSCO assess genome and annotation completeness - title_md: busco - - description_md: Contig Annotation Tool (CAT) - title_md: cat - - description_md: simple tool for removing duplicates from sequencing reads - title_md: cd_hit_dup - - description_md: Cluster or compare biological sequence datasets - title_md: cdhit - - description_md: Gene co-expression network analysis tool - title_md: cemitool - - description_md: Assess the quality of microbial genomes recovered from isolates, - single cells, and metagenomes - title_md: checkm - - description_md: Symphonizing pileup and full-alignment for high-performance long-read - variant calling - title_md: clair3 - - description_md: 'NoD: a Nucleolar localization sequence detector for eukaryotic - and viral proteins' - title_md: clinod - - description_md: ClustalW multiple sequence alignment program for DNA or proteins - title_md: clustalw - - description_md: removes lower scoring overlaps from cmsearch results. - title_md: cmsearch_deoverlap - - description_md: Detects positive selection - title_md: codeml - - description_md: co-occurrence of mutations on amplicons - title_md: cojac - - description_md: Combine multiple Assemblystats datasets into a single tabular - report - title_md: combine_assembly_stats - - description_md: Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species - abundances and gene families/pathways abundances - title_md: combine_metaphlan_humann - - description_md: Compare outputs of HUMAnN2 for several samples and extract similar - and specific information - title_md: compare_humann2_output - - description_md: 'Compleasm: a faster and more accurate reimplementation of BUSCO' - title_md: compleasm - - description_md: 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. - title_md: concoct - - description_md: CoverM genome and contig wrappers - title_md: coverm - - description_md: CryptoGenotyper is a standalone tool to *in-silico* determine - species and subtype based on SSU rRNA and gp60 markers. - title_md: cryptogenotyper - - description_md: Flexible tool to remove adapter sequences (and quality trim) high - throughput sequencing reads (fasta/fastq). - title_md: cutadapt - - description_md: DADA2 wrappers - title_md: dada2 - - description_md: DAS Tool for genome resolved metagenomics - title_md: das_tool - - description_md: Differential gene expression analysis based on the negative binomial - distribution - title_md: deseq2 - - description_md: DIAMOND is a new alignment tool for aligning short DNA sequencing - reads to a protein reference database such as NCBI-NR. - title_md: diamond - - description_md: DISCO is a overlap-layout-consensus (OLC) metagenome assembler - title_md: disco - - description_md: DRAM for distilling microbial metabolism to automate the curation - of microbiome function - title_md: dram - - description_md: dRep compares and dereplicates genome sets - title_md: drep - - description_md: EC-Typer - in silico serotyping of Escherichia coli species - title_md: ectyper - - description_md: Find bacterial type III effectors in protein sequences - title_md: effectiveT3 - - description_md: eggnog-mapper fast functional annotation of novel sequences - title_md: eggnog_mapper - - description_md: Galaxy wrappers for EMBOSS version 5.0.0 tools - title_md: emboss_5 - - description_md: Analyse phylogenetic trees using the ETE Toolkit - title_md: ete - - description_md: export2graphlan is a conversion software tool for producing both - annotation and tree file for GraPhlAn - title_md: export2graphlan - - description_md: ggplot2 histograms and density plots - title_md: ez_histograms - - description_md: fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) - title_md: fargene - - description_md: Fast alignment-free computation of whole-genome Average Nucleotide - Identity - title_md: fastani - - description_md: 'FastK: A K-mer counter (for HQ assembly data sets)' - title_md: fastk - - description_md: Fast all-in-one preprocessing for FASTQ files - title_md: fastp - - description_md: FASTQE - title_md: fastqe - - description_md: FastTree infers approximately-maximum-likelihood phylogenetic - trees from alignments of nucleotide or protein sequences - GVL - title_md: fasttree - - description_md: featureCounts counts the number of reads aligned to defined masked - regions in a reference genome - title_md: featurecounts - - description_md: Remove short and repeat contigs/scaffolds - title_md: filter_spades_repeats - - description_md: Filtlong - Filtering long reads by quality - title_md: filtlong - - description_md: FlashLFQ mass-spectrometry proteomics label-free quantification - title_md: flashlfq - - description_md: Assembly of long and error-prone reads. - title_md: flye - - description_md: Format MetaPhlAn2 output to extract abundance at different taxonomic - levels - title_md: format_metaphlan2_output - - description_md: Tool for finding (fragmented) genes in short read - title_md: fraggenescan - - description_md: lineage abundances estimation - title_md: freyja - - description_md: Suite for metabarcoding analysis - title_md: frogs - - description_md: Funannotate is a genome prediction, annotation, and comparison - software package. - title_md: funannotate - - description_md: Download MLST datasets by species from pubmlst.org - title_md: getmlst - - description_md: ggplot2 is a system for declaratively creating graphics, based - on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables - to aesthetics, what graphical primitives to use,and it takes care of the details. - title_md: ggplot2 - - description_md: Fetch taxonomic representation - title_md: gi2taxonomy - - description_md: Glimmer makes gene predictions. - title_md: glimmer - - description_md: GlimmerHMM is a new gene finder based on a Generalized Hidden - Markov Model (GHMM) - title_md: glimmer_hmm - - description_md: Performs GO Enrichment analysis. - title_md: goenrichment - - description_md: goseq does selection-unbiased testing for category enrichment - amongst differentially expressed (DE) genes for RNA-seq data - title_md: goseq - - description_md: GraPhlAn is a software tool for producing high-quality circular - representations of taxonomic and phylogenetic trees - title_md: graphlan - - description_md: Mapper for long, error-prone reads. - title_md: graphmap - - description_md: 'GTDB-Tk is a software tool kit for assigning objective taxonomic - classifications to bacterial and archaeal genomesbased on the Genome Database - Taxonomy GTDB. It is designed to work with recent advances that allow hundreds - orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from - environmental samples. It can alsobe applied to isolate and single-cell genomes. ' - title_md: gtdbtk - - description_md: Gubbins - bacterial recombination detection - title_md: gubbins - - description_md: Convert AMR gene detection tool output to hAMRonization specification - format. - title_md: hamronization - - description_md: Heidelberg and Enteritidis SNP Elucidation - title_md: hansel - - description_md: A hifiasm fork for metagenome assembly using Hifi reads. - title_md: hifiasm_meta - - description_md: An application that identifies potential transmission clusters - within a supplied FASTA file with an option to find potential links against - the Los Alamos HIV Sequence Database. - title_md: hivtrace - - description_md: HMMER is used for searching sequence databases for homologs of - proteinsequences, and for making protein sequence alignments. It implementsmethods - using probabilistic models called profile hidden Markov models(profile HMMs). - title_md: hmmer3 - - description_md: HUMAnN for functionally profiling metagenomes and metatranscriptomes - at species-level resolution - title_md: humann - - description_md: Hypothesis Testing using Phylogenies - title_md: hyphy - - description_md: Super Fast & Accurate Polisher for Long Read Genome Assemblies - title_md: hypo - - description_md: ICEscreen identifies Integrative Conjugative Elements (ICEs) and - Integrative Mobilizable Elements (IMEs) in Bacillota genomes. - title_md: icescreen - - description_md: Wrappers for the idba assembler variants. - title_md: idba_ud - - description_md: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence - databases for RNA structure and sequence similarities. - title_md: infernal - - description_md: InStrain is a tool for analysis of co-occurring genome populations - from metagenomes - title_md: instrain - - description_md: '"IntegronFinder identify integrons with high accuracy and sensitivity.It - searches for attC sites using covariance models, for integron-integrases using - HMM profiles, and for other features (promoters, attI site) using pattern matching"' - title_md: integron_finder - - description_md: Interproscan queries the interpro database and provides annotations. - title_md: interproscan - - description_md: Interproscan queries the interpro database and provides annotations. - title_md: iprscan5 - - description_md: Efficient phylogenomic software by maximum likelihood - title_md: iqtree - - description_md: '"ISEScan is a pipeline to identify IS (Insertion Sequence) elements - in genome and metagenomebased on profile hidden Markov models constructed from - manually curated IS elements."' - title_md: isescan - - description_md: ITSx is an open source software utility to extract the highly - variable ITS1 and ITS2 subregions from ITS sequences. - title_md: itsx - - description_md: iVar is a computational package that contains functions broadly - useful for viral amplicon-based sequencing - title_md: ivar - - description_md: JBrowse Genome Browser integrated as a Galaxy Tool - title_md: jbrowse - - description_md: Jellyfish is a tool for fast, memory-efficient counting of k-mers - in DNA - title_md: jellyfish - - description_md: Filtering kmers or reads from a database of kmers hashes - title_md: kat_filter - - description_md: Kc-Align custom tool - title_md: kc-align - - description_md: In-memory nucleotide sequence k-mer counting, filtering, graph - traversal and more - title_md: khmer - - description_md: Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella - pneumoniae species complex (KpSC) - title_md: kleborate - - description_md: Gene function annotation tool based on KEGG Orthology and hidden - Markov model - title_md: kofamscan - - description_md: Kraken is a system for assigning taxonomic labels to short DNAsequences, - usually obtained through metagenomic studies. Previous attempts by otherbioinformatics - software to accomplish this task have often used sequence alignmentor machine - learning techniques that were quite slow, leading to the developmentof less - sensitive but much faster abundance estimation programs. Kraken aims toachieve - high sensitivity and high speed by utilizing exact alignments of k-mersand a - novel classification algorithm. - title_md: kraken - - description_md: Kraken2 for taxonomic designation. - title_md: kraken2 - - description_md: Convert Kraken output to Galaxy taxonomy data. - title_md: kraken2tax - - description_md: Create BIOM-format tables (http://biom-format.org) from Kraken - output (http://ccb.jhu.edu/software/kraken/) - title_md: kraken_biom - - description_md: Kraken taxonomy report - title_md: kraken_taxonomy_report - - description_md: KrakenTools is a suite of scripts to be used alongside the Kraken - title_md: krakentools - - description_md: Predict MLST directly from uncorrected long reads - title_md: krocus - - description_md: Find lowest diagnostic rank - title_md: lca_wrapper - - description_md: Performs in silico Legionella pneumophila sequence based typing. - title_md: legsta - - description_md: Lighter is a kmer-based error correction method for whole genome - sequencing data - title_md: lighter - - description_md: Perform RNA-Seq differential expression analysis using limma voom - pipeline - title_md: limma_voom - - description_md: Identification of SARS-CoV-2 related metagenomic mutations based - on a single (or a list of) variant(s) file(s) - title_md: lineagespot - - description_md: Tools for M. tuberculosis DNA fingerprinting (spoligotyping) - title_md: lorikeet - - description_md: LotuS2 OTU processing pipeline - title_md: lotus2 - - description_md: m6anet to detect m6A RNA modifications from nanopore data - title_md: m6anet - - description_md: MaAsLin2 is comprehensive R package for efficiently determining - multivariable association between microbial meta'omic features and clinical - metadata. - title_md: maaslin2 - - description_md: Multiple alignment program for amino acid or nucleotide sequences - title_md: mafft - - description_md: Make a FASTA file non-redundant - title_md: make_nr - - description_md: MAKER is a portable and easily configurable genome annotation - pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects - to independently annotate their genomes and to create genome databases. - title_md: maker - - description_md: fast and accurate sequence read classification tool designed to - assign taxonomy and OTU classifications to ribosomal RNA sequences. - title_md: mapseq - - description_md: Fast genome and metagenome distance estimation using MinHash - title_md: mash - - description_md: clusters metagenomic contigs into bins - title_md: maxbin2 - - description_md: wrapper for MaxQuant - title_md: maxquant - - description_md: The Markov Cluster Algorithm, a cluster algorithm for graphs - title_md: mcl - - description_md: Sequence correction provided by ONT Research - title_md: medaka - - description_md: An ultra-fast single-node solution for large and complex metagenomics - assembly via succinct de Bruijn graph. - title_md: megahit - - description_md: A subprogram within the Megahit toolkit for converting contigs - to assembly graphs (fastg) - title_md: megahit_contig2fastg - - description_md: 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). - title_md: megan - - description_md: Assign sequence type to N. meningitidis genome assemblies - title_md: meningotype - - description_md: Merqury is a tool for evaluating genomes assemblies based of k-mer - operations. - title_md: merqury - - description_md: Meryl a k-mer counter. - title_md: meryl - - description_md: MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide - frequency) is an automated metagenome binningsoftware that integrates empirical - probabilistic distances of genome abundance and tetranucleotide frequency. - title_md: metabat2 - - description_md: 'MetaEuk is a modular toolkit designed for large-scale gene discovery - andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive - homology search capabilities of MMseqs2 with a dynamic programmingprocedure - to recover optimal exons sets. It reduces redundancies in multiplediscoveries - of the same gene and resolves conflicting gene predictions onthe same strand. ' - title_md: metaeuk - - description_md: MetaGeneAnnotator gene-finding program for prokaryote and phage - title_md: metagene_annotator - - description_md: metagenomeSeq Normalization - title_md: metagenomeseq - - description_md: Produce targeted databases for mass spectrometry analysis. - title_md: metanovo - - description_md: MetaPhlAn for Metagenomic Phylogenetic Analysis - title_md: metaphlan - - description_md: quantitative analysis of microbiome taxonomy and function - title_md: metaquantome - - description_md: A flexible pipeline for genome-resolved metagenomic data analysis - title_md: metawrapmg - - description_md: Short-read assembler based on a de Bruijn graph - title_md: minia - - description_md: Miniasm - Ultrafast de novo assembly for long noisy reads (though - having no consensus step) - title_md: miniasm - - description_md: Polishing miniasm assemblies - title_md: minipolish - - description_md: Align a protein sequence against a genome with affine gap penalty, - splicing and frameshift. - title_md: miniprot - - description_md: de-novo annotation of metazoan mitochondrial genomes - title_md: mitos - - description_md: Scan contig files against PubMLST typing schemes - title_md: mlst - - description_md: MOB-suite is a set of software tools for clustering, reconstruction - and typing of plasmids from draft assemblies - title_md: mob_suite - - description_md: Mothur wrappers - title_md: mothur - - description_md: A program for the Bayesian estimation of phylogeny. - title_md: mrbayes - - description_md: msconvert Convert and/or filter mass spectrometry files (including - vendor formats) using the official Docker container - title_md: msconvert - - description_md: MSstatsTMT protein significance analysis in shotgun mass spectrometry-based - proteomic experiments with tandem mass tag (TMT) labeling - title_md: msstatstmt - - description_md: GSEA-based pathway enrichment analysis for multi-omics data - title_md: multigsea - - description_md: MultiQC aggregates results from bioinformatics analyses across - many samples into a single report - title_md: multiqc - - description_md: Antibiotic resistance predictions - title_md: mykrobe - - description_md: RScript to parse the results of mykrobe predictor. - title_md: mykrobe_parser - - description_md: Creates a SQLite database for proteomics data - title_md: mz_to_sqlite - - description_md: Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets - from different experimental conditions expected to have a significant impact - on RNA modifications. It is recommended to have at least 2 replicates per condition. - For example one can use a control condition with a significantly reduced number - of modifications such as a cell line for which a modification writing enzyme - was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts - of interests could be synthesized in-vitro. - title_md: nanocompore - - description_md: Plotting tool for long read sequencing data and alignments - title_md: nanoplot - - description_md: NanopolishComp contains 2 modules. Eventalign_collapse collapses - the raw file generated by nanopolish eventalign by kmers rather than by event. - Freq_meth_calculate methylation frequency at genomic CpG sites from the output - of nanopolish call-methylation. - title_md: nanopolishcomp - - description_md: NCBI BLAST+ - title_md: ncbi_blast_plus - - description_md: FCS-GX detects contamination from foreign organisms in genome - sequences using the genome cross-species aligner (GX). - title_md: ncbi_fcs_gx - - description_md: Perform operations on Newick trees - title_md: newick_utils - - description_md: Identify differences between your sequences and a reference sequence - used by Nextstrain - title_md: nextclade - - description_md: String graph-based de novo assembler for long reads - title_md: nextdenovo - - description_md: Estimate average coverage in metagenomic datasets - title_md: nonpareil - - description_md: Prediction of Nucleosomes Positions on the Genome - title_md: nucleosome_prediction - - description_md: Marks/removes PCR introduced duplicate molecules based on the - molecular tagging technology used in NuGEN products. - title_md: nugen_nudup - - description_md: Compute biodiveristy indicators for marine data from obis - title_md: obisindicators - - description_md: OBITools is a set of programs developed to simplify the manipulation - of sequence files - title_md: obitools - - description_md: Proteome quality assessment software - title_md: omark - - description_md: Galaxy wrapper for ORFIPY - title_md: orfipy - - description_md: Accurate inference of orthologous gene groups made easy - title_md: orthofinder - - description_md: PeptideShaker and SearchGUI - title_md: peptideshaker - - description_md: Search a FASTA sequence against a library of Pfam HMM. - title_md: pfamscan - - description_md: rapid standardised annotation tool for bacteriophage genomes and - metagenomes - title_md: pharokka - - description_md: Handling and analysis of high-throughput microbiome census data - title_md: phyloseq - - description_md: PhyML is a phylogeny software based on the maximum-likelihood - principle. - title_md: phyml - - description_md: PICRUSt wrappers - title_md: picrust - - description_md: 'PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction - of Unobserved States' - title_md: picrust2 - - description_md: PlasFlow - Prediction of plasmid sequences in metagenomic contigs. - title_md: plasflow - - description_md: '"PlasmidFinder provides the detection of replicons in the WGSand - assigns the plasmids under study to lineages that trace backthe information - to the existing knowledge on Inc groups and suggestspossible reference plasmids - for each lineage"' - title_md: plasmidfinder - - description_md: Genome assembler for assemblying plasmid - title_md: plasmidspades - - description_md: '"Polypolish is a tool for polishing genome assemblies with short - reads.Polypolish uses SAM files where each read has been aligned to all possible - locations (not just a single best location).This allows it to repair errors - in repeat regions that other alignment-based polishers cannot fix."' - title_md: polypolish - - description_md: A protein-coding gene prediction software tool for bacterial and - archaeal genomes - title_md: prodigal - - description_md: Rapid annotation of prokaryotic genomes - title_md: prokka - - description_md: Aligns two sets of contigs and reports amino acid substitutions - between them - title_md: promer - - description_md: Proteinortho is a tool to detect orthologous proteins/genes within - different species. - title_md: proteinortho - - description_md: QC metrics for ONT Basecalling - title_md: pycoqc - - description_md: 'pyGenomeTracks: Standalone program and library to plot beautiful - genome browser tracks.' - title_md: pygenometracks - - description_md: QIIME to perform microbial community analysis - title_md: qiime_add_on - - description_md: QIIME to perform microbial community analysis - title_md: qiime_core - - description_md: Qualimap 2 is a platform-independent application written in Java - andR that facilitates the quality control of alignment sequencing data and itsderivatives - like feature counts. - title_md: qualimap - - description_md: Quast (Quality ASsessment Tool) evaluates genome assemblies. - title_md: quast - - description_md: Merge long-read and hybrid assemblies to increase contiguity - title_md: quickmerge - - description_md: Identification of ribosomal RNA genes in metagenomic fragments. - title_md: rRNA - - description_md: Consensus module for raw de novo DNA assembly of long uncorrected - reads. - title_md: racon - - description_md: Randomly subsample sequencing reads to a specified coverage - title_md: rasusa - - description_md: RAxML - A Maximum Likelihood based phylogenetic inference - title_md: raxml - - description_md: Rapid decontamination of SARS-CoV-2 sequencing reads - title_md: read_it_and_keep - - description_md: Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic - data. - title_md: reago - - description_md: '"With Recentrifuge, researchers can analyze results from taxonomic - classifiers using interactive charts with emphasis on the confidence level of - the classifications.In addition to contamination-subtracted samples.Recentrifuge - provides shared and exclusive taxa per sample,thus enabling robust contamination - removal and comparative analysis in environmental and clinical metagenomics."' - title_md: recentrifuge - - description_md: Tool for annotation of repeats from unassembled shotgun reads. - title_md: repeatexplorer2 - - description_md: Roary the pangenome pipeline - title_md: roary - - description_md: an RNA-seq quality control package - title_md: rseqc - - description_md: Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq and single-cell data. - title_md: salmon - - description_md: sarscov2formatter custom script - title_md: sarscov2formatter - - description_md: sarscov2summary custom script - title_md: sarscov2summary - - description_md: Scoary calculates the assocations between all genes in the accessory - genome and the traits. - title_md: scoary - - description_md: 'SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural - Networks' - title_md: semibin - - description_md: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - title_md: seqkit - - description_md: Tool for merging paired-end Illumina reads and trimming adapters. - title_md: seqprep - - description_md: Salmonella serotype prediction from genome sequencing data - title_md: seqsero2 - - description_md: Reconstruct haplotypes using ShoRAH in amplicon mode - title_md: shorah - - description_md: Faster de novo assembly pipeline based around Spades - title_md: shovill - - description_md: SISTR in silico serotyping tool - title_md: sistr_cmd - - description_md: Set of utilities for manipulating small viral genome data. - title_md: smallgenomeutilities - - description_md: SMALT aligns DNA sequencing reads with a reference genome. - title_md: smalt - - description_md: SNAP is a general purpose gene finding program suitable for both - eukaryotic and prokaryotic genomes. - title_md: snap - - description_md: Contains the snippy tool for characterising microbial snps - title_md: snippy - - description_md: Scripts for parsing Mykrobe predict results for Shigella sonnei. - title_md: sonneityping - - description_md: SortMeRNA is a software designed to rapidly filter ribosomal RNA - fragments from metatransriptomic data produced by next-generation sequencers. - title_md: sortmerna - - description_md: '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.' - title_md: spades - - description_md: SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping - from sequence reads - title_md: spotyping - - description_md: bowtie wrapper tool to align small RNA sequencing reads - title_md: sr_bowtie - - description_md: Short Read Sequence Typing for Bacterial Pathogens - title_md: srst2 - - description_md: SRST2 Short Read Sequence Typing for Bacterial Pathogens - title_md: srst2 - - description_md: Scan genome contigs against the ResFinder, PlasmidFinder, and - PointFinder antimicrobial resistance databases. - title_md: staramr - - description_md: Rapid and accurate identification of the sequence type (ST) - title_md: stringmlst - - description_md: for using multi-locus genotype data to investigate population - structure. - title_md: structure - - description_md: .nan - title_md: suite_qiime2__alignment - - description_md: .nan - title_md: suite_qiime2__composition - - description_md: .nan - title_md: suite_qiime2__cutadapt - - description_md: .nan - title_md: suite_qiime2__dada2 - - description_md: .nan - title_md: suite_qiime2__deblur - - description_md: .nan - title_md: suite_qiime2__demux - - description_md: .nan - title_md: suite_qiime2__diversity - - description_md: .nan - title_md: suite_qiime2__diversity_lib - - description_md: .nan - title_md: suite_qiime2__emperor - - description_md: .nan - title_md: suite_qiime2__feature_classifier - - description_md: .nan - title_md: suite_qiime2__feature_table - - description_md: .nan - title_md: suite_qiime2__fragment_insertion - - description_md: .nan - title_md: suite_qiime2__longitudinal - - description_md: .nan - title_md: suite_qiime2__metadata - - description_md: .nan - title_md: suite_qiime2__phylogeny - - description_md: .nan - title_md: suite_qiime2__quality_control - - description_md: .nan - title_md: suite_qiime2__quality_filter - - description_md: .nan - title_md: suite_qiime2__rescript - - description_md: .nan - title_md: suite_qiime2__sample_classifier - - description_md: .nan - title_md: suite_qiime2__taxa - - description_md: .nan - title_md: suite_qiime2__vsearch - - description_md: .nan - title_md: suite_qiime2_core - - description_md: .nan - title_md: suite_qiime2_core__tools - - description_md: Draw phylogeny - title_md: t2ps - - description_md: Summarize taxonomy - title_md: t2t_report - - description_md: T-Coffee - title_md: t_coffee - - description_md: Krona pie chart from taxonomic profile - title_md: taxonomy_krona_chart - - description_md: Processes M. tuberculosis sequence data to infer strain type and - identify known drug resistance markers. - title_md: tb-profiler - - description_md: ToolDistillator extract and aggregate information from different - tool outputs to JSON parsable files - title_md: tooldistillator - - description_md: TRANSIT - title_md: transit - - description_md: Finds rho-independent transcription terminators in bacterial genomes - title_md: transtermhp - - description_md: Trim Galore adaptive quality and adapter trimmer - title_md: trim_galore - - description_md: Trycycler toolkit wrappers - title_md: trycycler - - description_md: Unicycler is a hybrid assembly pipeline for bacterial genomes. - title_md: unicycler - - description_md: Unipept retrieves metaproteomics information - title_md: unipept - - description_md: Download UniProt proteome in XML or fasta format - title_md: uniprotxml_downloader - - description_md: UShER toolkit wrappers - title_md: usher - - description_md: A pipeline for detecting mis-assemblies in metagenomic assemblies. - title_md: valet - - description_md: Classify Influenza samples from raw short read sequence data - title_md: vapor - - description_md: Variable VirusAMPlicons (varVAMP) is a tool to design primers - for highly diverse viruses - title_md: varvamp - - description_md: an R package fo community ecologist - title_md: vegan - - description_md: de novo genomic assembler specially designed for short read sequencing - technologies - title_md: velvet - - description_md: Automatically optimize Velvet assemblies - title_md: velvet_optimiser - - description_md: virAnnot wrappers - title_md: virAnnot - - description_md: VSEARCH including searching, clustering, chimera detection, dereplication, - sorting, masking and shuffling of sequences. - title_md: vsearch - - description_md: WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads - assembly. - title_md: wtdbg - id: tool_list +- id: tool_list title: List of community curated tools available for microGalaxy -title: Community Tools + content: + - title_md: PAMPA + description_md: Tools to compute and analyse biodiversity metrics + - title_md: TreeBest + description_md: TreeBeST best + - title_md: abacas + description_md: Order and Orientate Contigs + - title_md: abricate + description_md: Mass screening of contigs for antiobiotic resistance genes