From 3d4def01911cbd86f2305c6e338c6713d1450a8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 23 Jul 2025 15:35:18 +0200 Subject: [PATCH 1/7] Update microGalaxy lab --- .../lab/sections/2_microbial_isolates.yml | 1052 +++---- .../microgalaxy/lab/sections/3_microbiome.yml | 1125 +++---- .../microgalaxy/lab/sections/4_tools.yml | 454 ++- .../microgalaxy/lab/sections/5_workflows.yml | 894 ++++-- .../microgalaxy/lab/tools/all/APOSTL.yaml | 118 +- .../microgalaxy/lab/tools/all/BioBix.yaml | 2653 +++++++++++++++++ .../microgalaxy/lab/tools/all/CIRM-CFBP.yaml | 118 +- .../microgalaxy/lab/tools/all/ChemFlow.yaml | 118 +- .../lab/tools/all/Coloc-stats.yaml | 118 +- .../microgalaxy/lab/tools/all/CorGAT.yaml | 118 +- .../microgalaxy/lab/tools/all/CoralSNP.yaml | 118 +- .../microgalaxy/lab/tools/all/CropGalaxy.yaml | 118 +- .../microgalaxy/lab/tools/all/Dintor.yaml | 118 +- .../lab/tools/all/FreeBioinfo.yaml | 118 +- .../microgalaxy/lab/tools/all/GASLINI.yaml | 118 +- .../lab/tools/all/Galaxy@AuBi.yaml | 115 +- .../lab/tools/all/Galaxy@Pasteur.yaml | 118 +- .../lab/tools/all/GalaxyTrakr.yaml | 94 +- .../lab/tools/all/Genomic_Hyperbrowser.yaml | 118 +- .../microgalaxy/lab/tools/all/GigaGalaxy.yaml | 118 +- .../lab/tools/all/IPK_Galaxy_Blast_Suite.yaml | 135 +- .../lab/tools/all/ImmPort_Galaxy.yaml | 118 +- .../lab/tools/all/InteractoMIX.yaml | 118 +- .../tools/all/Lebanese_University_Galaxy.yaml | 135 +- .../lab/tools/all/MISSISSIPPI.yaml | 118 +- .../lab/tools/all/MiModD_NacreousMap.yaml | 118 +- .../microgalaxy/lab/tools/all/Oqtans.yaml | 118 +- .../microgalaxy/lab/tools/all/Palfinder.yaml | 118 +- .../microgalaxy/lab/tools/all/PepSimili.yaml | 118 +- .../lab/tools/all/PhagePromotor.yaml | 118 +- .../lab/tools/all/UseGalaxy_be.yaml | 112 +- .../lab/tools/all/UseGalaxy_cz.yaml | 102 +- .../lab/tools/all/UseGalaxy_eu.yaml | 76 +- .../lab/tools/all/UseGalaxy_fr.yaml | 132 +- .../lab/tools/all/UseGalaxy_no.yaml | 115 +- .../lab/tools/all/UseGalaxy_org_Main.yaml | 144 +- .../lab/tools/all/UseGalaxy_org_au.yaml | 136 +- .../all/Viral_Variant_Visualizer_VVV.yaml | 118 +- .../microgalaxy/lab/tools/top/APOSTL.yaml | 464 ++- .../microgalaxy/lab/tools/top/BioBix.yaml | 1300 ++++++++ .../microgalaxy/lab/tools/top/CIRM-CFBP.yaml | 464 ++- .../microgalaxy/lab/tools/top/ChemFlow.yaml | 464 ++- .../lab/tools/top/Coloc-stats.yaml | 464 ++- .../microgalaxy/lab/tools/top/CorGAT.yaml | 464 ++- .../microgalaxy/lab/tools/top/CoralSNP.yaml | 464 ++- .../microgalaxy/lab/tools/top/CropGalaxy.yaml | 464 ++- .../microgalaxy/lab/tools/top/Dintor.yaml | 464 ++- .../lab/tools/top/FreeBioinfo.yaml | 464 ++- .../microgalaxy/lab/tools/top/GASLINI.yaml | 464 ++- .../lab/tools/top/Galaxy@AuBi.yaml | 454 ++- .../lab/tools/top/Galaxy@Pasteur.yaml | 452 ++- .../lab/tools/top/GalaxyTrakr.yaml | 156 +- .../lab/tools/top/Genomic_Hyperbrowser.yaml | 464 ++- .../microgalaxy/lab/tools/top/GigaGalaxy.yaml | 464 ++- .../lab/tools/top/IPK_Galaxy_Blast_Suite.yaml | 506 +++- .../lab/tools/top/ImmPort_Galaxy.yaml | 464 ++- .../lab/tools/top/InteractoMIX.yaml | 464 ++- .../tools/top/Lebanese_University_Galaxy.yaml | 506 +++- .../lab/tools/top/MISSISSIPPI.yaml | 179 +- .../lab/tools/top/MiModD_NacreousMap.yaml | 464 ++- .../microgalaxy/lab/tools/top/Oqtans.yaml | 464 ++- .../microgalaxy/lab/tools/top/Palfinder.yaml | 464 ++- .../microgalaxy/lab/tools/top/PepSimili.yaml | 464 ++- .../lab/tools/top/PhagePromotor.yaml | 464 ++- .../lab/tools/top/UseGalaxy_be.yaml | 192 +- .../lab/tools/top/UseGalaxy_cz.yaml | 123 +- .../lab/tools/top/UseGalaxy_eu.yaml | 99 +- .../lab/tools/top/UseGalaxy_fr.yaml | 40 +- .../lab/tools/top/UseGalaxy_no.yaml | 149 +- .../lab/tools/top/UseGalaxy_org_Main.yaml | 184 +- .../lab/tools/top/UseGalaxy_org_au.yaml | 146 +- .../top/Viral_Variant_Visualizer_VVV.yaml | 460 ++- 72 files changed, 18298 insertions(+), 5534 deletions(-) create mode 100644 communities/microgalaxy/lab/tools/all/BioBix.yaml create mode 100644 communities/microgalaxy/lab/tools/top/BioBix.yaml diff --git a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml index 4bb421d1f..67225cc19 100644 --- a/communities/microgalaxy/lab/sections/2_microbial_isolates.yml +++ b/communities/microgalaxy/lab/sections/2_microbial_isolates.yml @@ -3,491 +3,491 @@ title: Microbial isolates tabs: - id: overview title: Overview - heading_md: > - Microbial isolates data analysis can encompass genomics, transcriptomics, and proteomics. These analyses (from raw data to differential analyses or visualization via assembly) are supported in microGalaxy with different tool suites and potential analyses available on microGalaxy. + heading_md: "Microbial isolates data analysis can encompass genomics, transcriptomics, + and proteomics. These analyses (from raw data to differential analyses or visualization + via assembly) are supported in microGalaxy with different tool suites and potential + analyses available on microGalaxy. \n" content: - - title_md: "Overview of possible microbial isolates data analysis tasks with corresponding tool suites and potential analysis available on microGalaxy" - description_md: | -
- Overview of microbial isolates data analysis -

- - Outputs are color-coded by type and numbers indicate available tool suites for each step. - - Input data (blue) represent raw datasets, including sequencing reads and mass spectra. - Intermediate outputs (gray) include cleaned reads, assemblies, and OTUs/AVSs. - Taxonomic outputs (green) represent taxonomic profiling results. - Functional outputs (yellow) highlight functional profiling and differential feature analysis. - Other outputs (orange) indicate annotated genomes, reconstructed genomes, and antibiotic resistance genes. - - Numbers correspond to tool suites: - (1) falco, - FastQC, - Cutadapt, - fastp, - MultiQC, - Porechop, - Filtlong, - NanoPlot, - Pycoqc, - FastQE, - lighter, - Rasusa, - BBtools (e.g. BBMap), - SeqKit (e.g. SeqKut sort), - NCBI FCS GX, - Bowtie, - BWA, - minimap, - SortMeRNA, - - (2) MetaPhlAn, - Kraken2, - Bracken, - Diamond, - [soon] Sylph, - mOTUs, - (Re)Centrifuge, - GTDB-Tk, - VirAnnot, - Metabuli, - MEGAN (e.g. meganize a DIAMOND file) - - - (3) Shovill, - Unicycler, - SPades, - Flye, - SKESA, - ABySS, - Velvet (e.g. Velveth), - Racon, - Pilon, - Polypolish, - QUAST, - BUSCO, - CheckM (e.g. CheckM analyze) - - (4) Bakta, - Prokka, - Maker, - Prodigal, - braker, - eggNOG Mapper, - InterProScan, - Funannotate (e.g. Funannotate functional annotation), - pharokka, - - (5) HMMER - - (6) Bakta, - AMRFinderPlus, - ABRicate, - fARGene, - hAMRonization, - argNorm, - StarAMR, - abriTAMR, - TB-Profiler, - SeqSero2 - - (7) ABRicate - - (8) ISEScan, - Transit, - PlasmidFinder - - (9) StarAMR, - chewBBaca (e.g. chewBBaca create schema), - pyMLST (e.g. Add strain to cg/wgMLST database), - MLST, - SISTR - - (10) Integron Finder, - CRISPRCasFinder, - MITOS2 - - (11) antiSMASH, - HMMER - - (12) Gene Ontology, - KEGG - - (13) Orthofinder, - Proteinortho, - Roary, - Mauve, - Clustal (Omega), - FastTree, - RAxML, - Circos, - PPanGGolin, - panaroo - - (14) BWA, - Bowtie, - Minimap, - Picard Tools (e.g. Picard Collect Sequencing Artifact Metrics) - - (15) FreeBayes, - GATK, - Bcftools (e.g. BCFtools mpileup), - Snippy, - medaka (e.g. medaka consensus tool), - Clair3 - - (16) VCFtools (e.g. VCFcombine), - SnpSift (e.g. SnpSift Filter), - SnpEff (e.g. SnpEff build), - Samtools (e.g. Samtools coverage) - - (17) STAR (e.g. RNA STAR), - HISAT, - Bowtie - - (18) featureCounts, - HISAT - - (19) edgeR, - DESeq2 - - (20) StringTie, - GFFCompare, - Cufflinks - - (21) msconvert, - OpenMS (e.g. XTandemAdapter) - - (22) SearchGUI, - PeptideShaker, - MaxQuant, - FragPipe - - (23) MaxQuant, - PepQuery, - FragPipe, - MSstatsTMT, - iTRAQ, - UniPept - - (24) MSStats - -

- Note: If a tool link does not work or is missing, it may not be installed on this server. Please contact - support for assistance. - If a tool is not listed here and you cannot find it in the tool's panel, you can request it via the microGalaxy community: - microgalaxy@lists.galaxyproject.org. -

-
- + - title_md: Overview of possible microbial isolates data analysis tasks with corresponding + tool suites and potential analysis available on microGalaxy + description_md: "
\n \"Overview\n

\n\n Outputs are color-coded by type and numbers indicate + available tool suites for each step.\n\n Input data (blue) + represent raw datasets, including sequencing reads and mass spectra. \n \ + \ Intermediate outputs (gray) include cleaned reads, assemblies, + and OTUs/AVSs. \n Taxonomic outputs (green) represent + taxonomic profiling results. \n Functional outputs (yellow) + highlight functional profiling and differential feature analysis. \n + Other outputs (orange) indicate annotated genomes, reconstructed genomes, + and antibiotic resistance genes.\n\n Numbers correspond to tool + suites: \n (1) falco, \n FastQC, \n Cutadapt, \n fastp, \n MultiQC,\n Porechop, \n Filtlong, \n NanoPlot, \n Pycoqc, \n FastQE, \n lighter, \n Rasusa, \n BBtools (e.g. BBMap),\n SeqKit (e.g. SeqKut sort),\n NCBI FCS GX,\n Bowtie, \n BWA,\n minimap,\n SortMeRNA, \n\n (2) MetaPhlAn, \n Kraken2, \n Bracken, \n Diamond, \n [soon] Sylph, \n mOTUs, \n (Re)Centrifuge, \n GTDB-Tk,\n VirAnnot,\n Metabuli,\n MEGAN (e.g. meganize a DIAMOND file)\n \n\n (3) Shovill, \n Unicycler, \n SPades, \n Flye, \n SKESA, \n ABySS, \n Velvet (e.g. Velveth), \n Racon, \n Pilon, \n Polypolish, \n QUAST, \n BUSCO, \n CheckM (e.g. CheckM analyze) \n\n (4) Bakta, \n Prokka, \n Maker, \n Prodigal, \n braker,\n eggNOG Mapper,\n InterProScan,\n Funannotate (e.g. Funannotate functional annotation),\n pharokka,\n\n (5) HMMER \n\n (6) Bakta, \n AMRFinderPlus, \n ABRicate, \n fARGene, \n hAMRonization,\n argNorm, \n StarAMR, \n abriTAMR, \n TB-Profiler, \n SeqSero2\n\n (7) ABRicate\n\n (8) ISEScan, \n Transit, \n PlasmidFinder\n\n (9) StarAMR, \n chewBBaca (e.g. chewBBaca create schema), \n pyMLST (e.g. Add strain to cg/wgMLST database), \n MLST, \n SISTR \n\n (10) Integron Finder,\n CRISPRCasFinder,\n MITOS2 \n\n (11) antiSMASH, \n HMMER \n\n (12) Gene Ontology, \n KEGG\n \n (13) Orthofinder, \n Proteinortho, \n Roary, \n Mauve, \n Clustal (Omega), \n FastTree, \n RAxML, \n Circos, \n PPanGGolin, \n panaroo \n \n (14) BWA, \n Bowtie, \n Minimap, \n Picard Tools (e.g. Picard Collect Sequencing Artifact Metrics) \n \n\ + \ (15) FreeBayes, \n GATK, \n Bcftools (e.g. BCFtools mpileup), \n Snippy, \n medaka (e.g. medaka consensus tool), \n Clair3 \n\n (16) VCFtools (e.g. VCFcombine),\n SnpSift (e.g. SnpSift Filter),\n SnpEff (e.g. SnpEff build), \n Samtools (e.g. Samtools coverage) \n\n (17) STAR (e.g. RNA STAR), \n HISAT, \n Bowtie\n\n (18) featureCounts, \n HISAT \n\n (19) edgeR, \n DESeq2 \n\n (20) StringTie, \n GFFCompare, \n Cufflinks \n \n (21) msconvert, \n OpenMS (e.g. XTandemAdapter)\n\n (22) SearchGUI,\n PeptideShaker,\n MaxQuant,\n FragPipe\n\n (23) MaxQuant,\n PepQuery,\n FragPipe,\n MSstatsTMT,\n iTRAQ,\n UniPept \n\n (24) MSStats \n\n

\n Note: + If a tool link does not work or is missing, it may not be installed on this + server. Please contact \n support for assistance.\ + \ \n If a tool is not listed here and you cannot find it in the tool's panel, + you can request it via the microGalaxy community: \n microgalaxy@lists.galaxyproject.org.\n

\n
\n" - id: tools title: Tools - heading_md: > - Flagship tools for microbiome analysis + heading_md: "Flagship tools for microbiome analysis\n" content: subsections: - - id: genomics - title: Genomics - content: - - title_md: Shovill - A faster SPAdes assembly of Illumina reads - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill" - description_md: > - Microbial assembly pipeline for Illumina paired-end reads. - - title_md: Bakta - A rapid and standardized annotation of bacterial genomes, MAGs, and plasmids - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta" - description_md: > - It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis. Although Bakta conducts a more comprehensive workflow and provides a taxonomic-independent database that is several orders of magnitude larger, it is nevertheless as easy to use and almost as fast as Prokka. - - title_md: Clair3 - A germline small variant caller for long-reads - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3" - description_md: > - Clair3 is a symphonizing pileup and full alignment for high-performance long-read variant calling. - - title_md: AMRFinderPlus - An NCBI Antimicrobial Resistance Gene Finder - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus" - description_md: > - This tool and its accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. - - title_md: PPanGGoLin - Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors - description_md: > - PPanGGoLin is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. - - - title_md: antiSMASH - Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash" - description_md: > - Antismash allows the genome-wide identification, annotation, and analysis of secondary metabolite biosynthesis gene clusters - - - id: transcriptomics - title: Transcriptomics - content: - - title_md: Minimap - A fast pairwise aligner for genomic and spliced nucleotide sequences - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2" - description_md: > - Minimap is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. - - title_md: Bowtie - An ultrafast memory-efficient short read aligner - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2" - description_md: > - Bowtie is an ultrafast, memory-efficient short-read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. - - title_md: STAR - Gapped-read mapper for RNA-seq data - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star" - description_md: > - STAR is an aligner designed to specifically address many of the challenges of RNA-seq data mapping using a strategy to account for spliced alignments. - - title_md: featureCounts - An ultrafast and accurate read summarization program - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts" - description_md: > - featureCounts measures gene expression in RNA-Seq experiments from SAM or BAM files. - - title_md: GFFCompare - A tool that compares assembled transcripts to a reference annotation - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare" - description_md: > - GFFCompare can be used to compare, merge, annotate, and estimate the accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF). - - title_md: DESeq - Differential expression analysis for sequence count data - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2" - description_md: > - DESeq allows the analysis of experiments with no biological replicates in one or even both of the conditions. - - - id: proteomics - title: Proteomics - content: - - title_md: msconvert - A tool for converting and/or filtering mass spectrometry files - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert" - description_md: > - A tool to convert between various file formats, such as mzML, mz5, mgf, text, ms1, cms1, ms2, cms2, with many options. - - title_md: MaxQuant - A tool for analyzing large mass-spectrometric - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant" - description_md: > - MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. - - title_md: OpenMS - A framework for Mass Spectrometry - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter" - description_md: > - OpenMS offers C++ library (+ Python bindings) for LC/MS data management, analysis, and visualization. It empowers the rapid development of mass spectrometry-related software. - - title_md: Peptide Shaker - A tool that performs protein identification - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker" - description_md: > - Peptide Shaker uses various search engines based on results from SearchGUI - + - id: genomics + title: Genomics + content: + - title_md: Shovill - A faster SPAdes assembly of Illumina reads + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill' + description_md: "Microbial assembly pipeline for Illumina paired-end reads.\n" + - title_md: Bakta - A rapid and standardized annotation of bacterial + genomes, MAGs, and plasmids + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta' + description_md: "It provides dbxref-rich and sORF-including annotations in + machine-readable JSON & bioinformatics standard file formats for automatic + downstream analysis. Although Bakta conducts a more comprehensive workflow + and provides a taxonomic-independent database that is several orders of + magnitude larger, it is nevertheless as easy to use and almost as fast as + Prokka.\n" + - title_md: Clair3 - A germline small variant caller for long-reads + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3' + description_md: "Clair3 is a symphonizing pileup and full alignment for high-performance + long-read variant calling.\n" + - title_md: AMRFinderPlus - An NCBI Antimicrobial Resistance Gene + Finder + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus' + description_md: "This tool and its accompanying database are designed to find + acquired antimicrobial resistance genes and point mutations in protein and/or + assembled nucleotide sequences.\n" + - title_md: PPanGGoLin - Depicting microbial species diversity + via a Partitioned PanGenome Graph Of Linked Neighbors + description_md: "PPanGGoLin is a software suite used to create and manipulate + prokaryotic pangenomes from a set of either genomic DNA sequences or provided + genome annotations. It is designed to scale up to tens of thousands of genomes. + \n" + - title_md: antiSMASH - Rapid identification, annotation and analysis + of secondary metabolite biosynthesis gene clusters in bacterial and fungal + genome sequences + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash' + description_md: "Antismash allows the genome-wide identification, annotation, + and analysis of secondary metabolite biosynthesis gene clusters\n" + - id: transcriptomics + title: Transcriptomics + content: + - title_md: Minimap - A fast pairwise aligner for genomic and spliced + nucleotide sequences + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2' + description_md: "Minimap is a versatile sequence alignment program that aligns + DNA or mRNA sequences against a large reference database.\n" + - title_md: Bowtie - An ultrafast memory-efficient short read aligner + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2' + description_md: "Bowtie is an ultrafast, memory-efficient short-read aligner. + It aligns short DNA sequences (reads) to the human genome at a rate of over + 25 million 35-bp reads per hour.\n" + - title_md: STAR - Gapped-read mapper for RNA-seq data + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star' + description_md: "STAR is an aligner designed to specifically address many + of the challenges of RNA-seq data mapping using a strategy to account for + spliced alignments.\n" + - title_md: featureCounts - An ultrafast and accurate read summarization + program + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts' + description_md: "featureCounts measures gene expression in RNA-Seq experiments + from SAM or BAM files.\n" + - title_md: GFFCompare - A tool that compares assembled transcripts + to a reference annotation + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare' + description_md: "GFFCompare can be used to compare, merge, annotate, and estimate + the accuracy of one or more GFF files (the “query” files), when compared + with a reference annotation (also provided as GFF).\n" + - title_md: DESeq - Differential expression analysis for sequence + count data + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2' + description_md: "DESeq allows the analysis of experiments with no biological + replicates in one or even both of the conditions.\n" + - id: proteomics + title: Proteomics + content: + - title_md: msconvert - A tool for converting and/or filtering + mass spectrometry files + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert' + description_md: "A tool to convert between various file formats, such as mzML, + mz5, mgf, text, ms1, cms1, ms2, cms2, with many options.\n" + - title_md: MaxQuant - A tool for analyzing large mass-spectrometric + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant' + description_md: "MaxQuant is a quantitative proteomics software package designed + for analyzing large mass-spectrometric data sets. It is specifically aimed + at high-resolution MS data.\n" + - title_md: OpenMS - A framework for Mass Spectrometry + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter' + description_md: "OpenMS offers C++ library (+ Python bindings) for LC/MS data + management, analysis, and visualization. It empowers the rapid development + of mass spectrometry-related software.\n" + - title_md: Peptide Shaker - A tool that performs protein identification + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker' + description_md: "Peptide Shaker uses various search engines based on results + from SearchGUI\n" - id: interactive-tools title: Interactive tools - heading_md: > - Interactive tools for microbial research + heading_md: "Interactive tools for microbial research \n" content: - - title_md: RStudio - An integrated development environment (IDE) for R and Python - description_md: > - This familiar R analysis software suite will let you explore your datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr, LaTeX, bioconductor, cummeRbund, and many more pre-installed packages. - button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_rstudio" - - title_md: Interactive JupyterLab Notebook - A web-based interactive computing platform - description_md: > - The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. - inputs: - - datatypes: - - Jupyter Notebook - button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_jupyter_notebook" - + - title_md: RStudio - An integrated development environment (IDE) for + R and Python + description_md: "This familiar R analysis software suite will let you explore + your datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr, LaTeX, + bioconductor, cummeRbund, and many more pre-installed packages.\n" + button_link: '{{ galaxy_base_url }}/root?tool_id=interactive_tool_rstudio' + - title_md: Interactive JupyterLab Notebook - A web-based interactive + computing platform + description_md: "The Jupyter Notebook is an open-source web application that allows + you to create and share documents that contain live code, equations, visualizations, + and narrative text. Uses include: data cleaning and transformation, numerical + simulation, statistical modeling, data visualization, machine learning, and + much more.\n" + inputs: + - datatypes: + - Jupyter Notebook + button_link: '{{ galaxy_base_url }}/root?tool_id=interactive_tool_jupyter_notebook' - id: databases title: Databases - heading_md: Examples of databases prebuilt in some tools by microGalaxy. Even more databases are also found in microGalaxy, such as PhageDB, MAdLandDB, SwissProt, PDB, etc. + heading_md: Examples of databases prebuilt in some tools by microGalaxy. Even more + databases are also found in microGalaxy, such as PhageDB, MAdLandDB, SwissProt, + PDB, etc. content: subsections: - - id: genomic-databases - title: Genomic Databases - content: - - title_md: NCBI RefSeq - Reference genome database - button_link: "https://www.ncbi.nlm.nih.gov/refseq/" - button_tip: "Visit NCBI RefSeq" - description_md: > - A comprehensive collection of reference genomes for bacteria, archaea, and eukaryotes. - Used in tools such as [Prokka]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka) and [Bakta]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta). - - title_md: ENA - European Nucleotide Archive - button_link: "https://www.ebi.ac.uk/ena" - button_tip: "Visit ENA" - description_md: > - A primary repository for nucleotide sequencing data. - Used in tools such as [EBI Search]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results). - - title_md: NCBI GenBank - Public Sequence Database - button_link: "https://www.ncbi.nlm.nih.gov/genbank/" - button_tip: "Visit GenBank" - description_md: > - A comprehensive open-access collection of annotated nucleotide sequences. - Used in tools such as [Prokka]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka) and [Bakta]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta). - - - id: antibiotic-resistance-databases - title: Antibiotic Resistance Databases - content: - - title_md: CARD - Comprehensive Antibiotic Resistance Database - button_link: "https://card.mcmaster.ca/" - button_tip: "Visit CARD" - description_md: > - A manually curated reference database of antimicrobial resistance genes. - Used in tools such as [StarAMR]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search) and [AMRFinderPlus]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus). - - title_md: ResFinder - Identifies acquired antimicrobial resistance genes - button_link: "https://cge.food.dtu.dk/services/ResFinder/" - button_tip: "Visit ResFinder" - description_md: > - A tool for detecting antimicrobial resistance genes in bacterial genomes. - Used in tools such as [ABRicate]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate). - - title_md: NCBI AMRFinder - Antimicrobial Resistance Gene Finder - button_link: "https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" - button_tip: "Visit AMRFinder" - description_md: > - A tool and database for detecting acquired antimicrobial resistance genes in bacterial genomes. - Used in tools such as [AMRFinderPlus]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus). - - title_md: ARG-ANNOT - Antibiotic Resistance Gene Database - button_link: "https://www.mediterranee-infection.com/arg-annot-database/" - button_tip: "Visit ARG-ANNOT" - description_md: > - A database of resistance genes used for identifying antibiotic resistance determinants. - Used in tools such as [ABRicate]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate). - - - id: functional-annotation - title: Functional Annotation Databases - content: - - title_md: KEGG - Kyoto Encyclopedia of Genes and Genomes - button_link: "https://www.kegg.jp/" - button_tip: "Visit KEGG" - description_md: > - A comprehensive database of molecular interactions, reactions, and pathways. - Used in tools such as [KofamScan]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kofamscan/kofamscan). - - title_md: eggNOG - Orthologous gene groups database - button_link: "http://eggnog5.embl.de/" - button_tip: "Visit eggNOG" - description_md: > - A hierarchical database of orthologous gene families and functional annotation. - Used in tools such as [eggNOG-mapper]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper). - - title_md: MetaCyc - Metabolic pathways database - button_link: "https://metacyc.org/" - button_tip: "Visit MetaCyc" - description_md: > - A curated database of metabolic pathways and enzymes from all domains of life. - Used in tools such as [KOBAS Identify]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_identify). - - - id: transcriptomic-databases - title: Transcriptomic Databases - content: - - title_md: ArrayExpress - Functional Genomics Data Repository - button_link: "https://www.ebi.ac.uk/arrayexpress/" - button_tip: "Visit ArrayExpress" - description_md: > - A collection of transcriptomic and functional genomic datasets. - Used in tools such as [Limma]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom). - - - id: proteomic-databases - title: Proteomic Databases - content: - - title_md: UniProt - Universal Protein Knowledgebase - button_link: "https://www.uniprot.org/" - button_tip: "Visit UniProt" - description_md: > - A comprehensive protein sequence and functional information resource. - Used in tools such as [MaxQuant]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant). - - title_md: PRIDE - Proteomics Identification Database - button_link: "https://www.ebi.ac.uk/pride/" - button_tip: "Visit PRIDE" - description_md: > - A public repository for mass spectrometry-based proteomics data. - Used in tools such as [Peptide Shaker]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker). - + - id: genomic-databases + title: Genomic Databases + content: + - title_md: NCBI RefSeq - Reference genome database + button_link: https://www.ncbi.nlm.nih.gov/refseq/ + button_tip: Visit NCBI RefSeq + description_md: "A comprehensive collection of reference genomes for bacteria, + archaea, and eukaryotes. Used in tools such as [Prokka]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka) + and [Bakta]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta).\n" + - title_md: ENA - European Nucleotide Archive + button_link: https://www.ebi.ac.uk/ena + button_tip: Visit ENA + description_md: "A primary repository for nucleotide sequencing data. Used + in tools such as [EBI Search]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results).\n" + - title_md: NCBI GenBank - Public Sequence Database + button_link: https://www.ncbi.nlm.nih.gov/genbank/ + button_tip: Visit GenBank + description_md: "A comprehensive open-access collection of annotated nucleotide + sequences. Used in tools such as [Prokka]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka) and [Bakta]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta).\n" + - id: antibiotic-resistance-databases + title: Antibiotic Resistance Databases + content: + - title_md: CARD - Comprehensive Antibiotic Resistance Database + button_link: https://card.mcmaster.ca/ + button_tip: Visit CARD + description_md: "A manually curated reference database of antimicrobial resistance + genes. Used in tools such as [StarAMR]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search) + and [AMRFinderPlus]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus).\n" + - title_md: ResFinder - Identifies acquired antimicrobial resistance + genes + button_link: https://cge.food.dtu.dk/services/ResFinder/ + button_tip: Visit ResFinder + description_md: "A tool for detecting antimicrobial resistance genes in bacterial + genomes. Used in tools such as [ABRicate]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate).\n" + - title_md: NCBI AMRFinder - Antimicrobial Resistance Gene Finder + button_link: https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ + button_tip: Visit AMRFinder + description_md: "A tool and database for detecting acquired antimicrobial + resistance genes in bacterial genomes. Used in tools such as [AMRFinderPlus]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus).\n" + - title_md: ARG-ANNOT - Antibiotic Resistance Gene Database + button_link: https://www.mediterranee-infection.com/arg-annot-database/ + button_tip: Visit ARG-ANNOT + description_md: "A database of resistance genes used for identifying antibiotic + resistance determinants. Used in tools such as [ABRicate]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate).\n" + - id: functional-annotation + title: Functional Annotation Databases + content: + - title_md: KEGG - Kyoto Encyclopedia of Genes and Genomes + button_link: https://www.kegg.jp/ + button_tip: Visit KEGG + description_md: "A comprehensive database of molecular interactions, reactions, + and pathways. Used in tools such as [KofamScan]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kofamscan/kofamscan).\n" + - title_md: eggNOG - Orthologous gene groups database + button_link: http://eggnog5.embl.de/ + button_tip: Visit eggNOG + description_md: "A hierarchical database of orthologous gene families and + functional annotation. Used in tools such as [eggNOG-mapper]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper).\n" + - title_md: MetaCyc - Metabolic pathways database + button_link: https://metacyc.org/ + button_tip: Visit MetaCyc + description_md: "A curated database of metabolic pathways and enzymes from + all domains of life. Used in tools such as [KOBAS Identify]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_identify).\n" + - id: transcriptomic-databases + title: Transcriptomic Databases + content: + - title_md: ArrayExpress - Functional Genomics Data Repository + button_link: https://www.ebi.ac.uk/arrayexpress/ + button_tip: Visit ArrayExpress + description_md: "A collection of transcriptomic and functional genomic datasets. + Used in tools such as [Limma]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom).\n" + - id: proteomic-databases + title: Proteomic Databases + content: + - title_md: UniProt - Universal Protein Knowledgebase + button_link: https://www.uniprot.org/ + button_tip: Visit UniProt + description_md: "A comprehensive protein sequence and functional information + resource. Used in tools such as [MaxQuant]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant).\n" + - title_md: PRIDE - Proteomics Identification Database + button_link: https://www.ebi.ac.uk/pride/ + button_tip: Visit PRIDE + description_md: "A public repository for mass spectrometry-based proteomics + data. Used in tools such as [Peptide Shaker]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker).\n" - id: workflows title: Workflows - heading_md: Microbial isolates analysis workflows to use directly, modify or take ideas from + heading_md: Microbial isolates analysis workflows to use directly, modify or take + ideas from content: subsections: - - id: genomics - title: Genomics Workflows - content: - - title_md: Datasets Quality Control - description_md: > - General quality controlling workflow. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222" - button_tip: Import workflow - button_icon: run - - title_md: Assembly with Flye - description_md: > - Assemble long reads with Flye, then view assembly statistics and assembly graph. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=750" - button_tip: Import workflow - button_icon: run - - title_md: Bacterial Genome Assembly - description_md: > - Assembly of bacterial paired-end short read data with the generation of quality metrics and reports. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1043" - button_tip: Import workflow - button_icon: run - - title_md: Bacterial Genome Annotation - description_md: > - Annotation of assembled bacterial genomes to detect genes, potential plasmids, integrons, and Insertion sequence (IS) elements. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1050" - button_tip: Import workflow - button_icon: run - - title_md: Refining Genome Annotations with Apollo (prokaryotes) - description_md: > - Refining Genome Annotations with Apollo. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=749" - button_tip: Import workflow - button_icon: run - - title_md: Genome annotation workflow with Helixer - description_md: > - This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1255" - button_tip: Import workflow - button_icon: run - - title_md: AMR Gene detection - description_md: > - Antimicrobial resistance gene detection from assembled bacterial genomes. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1049" - button_tip: Import workflow - button_icon: run - - title_md: Phenotypic vs. In Silico AMR Detection in Salmonella enterica using StarAMR - description_md: > - Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using StarAMR. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=470" - button_tip: Import workflow - button_icon: run - - title_md: M. tuberculosis Variant Analysis - description_md: > - Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina). - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1035" - button_tip: Import workflow - button_icon: run - - - id: transcriptomics - title: Transcriptomics Workflows - content: - - title_md: mRNA-Seq BY-COVID Pipeline - description_md: > - Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=685" - button_tip: Import workflow - button_icon: run - - title_md: mRNA-Seq BY-COVID Pipeline Counts - description_md: > - This workflow produces sets of feature Counts ready for analysis by limma/etc. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=688" - button_tip: Import workflow - button_icon: run - - title_md: mRNA-Seq BY-COVID Pipeline Analysis - description_md: > - Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=689" - button_tip: Import workflow - button_icon: run - + - id: genomics + title: Genomics Workflows + content: + - title_md: Datasets Quality Control + description_md: "General quality controlling workflow.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222' + button_tip: Import workflow + button_icon: run + - title_md: Assembly with Flye + description_md: "Assemble long reads with Flye, then view assembly statistics + and assembly graph.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=750' + button_tip: Import workflow + button_icon: run + - title_md: Bacterial Genome Assembly + description_md: "Assembly of bacterial paired-end short read data with the + generation of quality metrics and reports.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1043' + button_tip: Import workflow + button_icon: run + - title_md: Bacterial Genome Annotation + description_md: "Annotation of assembled bacterial genomes to detect genes, + potential plasmids, integrons, and Insertion sequence (IS) elements.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1050' + button_tip: Import workflow + button_icon: run + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: "Refining Genome Annotations with Apollo.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=749' + button_tip: Import workflow + button_icon: run + - title_md: Genome annotation workflow with Helixer + description_md: "This workflow allows you to annotate a genome with Helixer + and evaluate the quality of the annotation using BUSCO and Genome Annotation + statistics. GFFRead is also used to predict protein sequences derived from + this annotation, and BUSCO and OMArk are used to assess proteome quality.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1255' + button_tip: Import workflow + button_icon: run + - title_md: AMR Gene detection + description_md: "Antimicrobial resistance gene detection from assembled bacterial + genomes.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1049' + button_tip: Import workflow + button_icon: run + - title_md: Phenotypic vs. In Silico AMR Detection in Salmonella enterica using + StarAMR + description_md: "Correlation between Phenotypic and In Silico Detection of + Antimicrobial Resistance in Salmonella enterica in Canada Using StarAMR.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=470' + button_tip: Import workflow + button_icon: run + - title_md: M. tuberculosis Variant Analysis + description_md: "Predict variants and drug resistance from M. tuberculosis + sequence samples (Illumina).\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1035' + button_tip: Import workflow + button_icon: run + - id: transcriptomics + title: Transcriptomics Workflows + content: + - title_md: mRNA-Seq BY-COVID Pipeline + description_md: "Analyse Bulk RNA-Seq data in preparation for downstream Pathways + analysis with MINERVA.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=685' + button_tip: Import workflow + button_icon: run + - title_md: mRNA-Seq BY-COVID Pipeline Counts + description_md: "This workflow produces sets of feature Counts ready for analysis + by limma/etc.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=688' + button_tip: Import workflow + button_icon: run + - title_md: mRNA-Seq BY-COVID Pipeline Analysis + description_md: "Analyse Bulk RNA-Seq data in preparation for downstream Pathways + analysis with MINERVA.\n" + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=689' + button_tip: Import workflow + button_icon: run - id: tutorials title: Tutorials heading_md: Tutorials to train you to perform microbial data analysis content: - - title_md: Making sense of a newly assembled genome - description_md: Tutorial stored in Assembly topic on the Galaxy Training Network - and covering topics related to Sequence assembly, Genomics, Microbiology - button_link: - https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html - button_tip: View tutorial - button_icon: tutorial - - title_md: Assembly of metagenomic sequencing data - description_md: Tutorial stored in Assembly topic on the Galaxy Training Network - and covering topics related to Metagenomics, Sequence assembly - button_link: - https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html - button_tip: View tutorial - button_icon: tutorial - title_md: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) description_md: Tutorial stored in Assembly topic on the Galaxy Training Network @@ -513,6 +513,20 @@ tabs: https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html button_tip: View tutorial button_icon: tutorial + - title_md: Assembly of metagenomic sequencing data + description_md: Tutorial stored in Assembly topic on the Galaxy Training Network + and covering topics related to Metagenomics, Sequence assembly + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html + button_tip: View tutorial + button_icon: tutorial + - title_md: Making sense of a newly assembled genome + description_md: Tutorial stored in Assembly topic on the Galaxy Training Network + and covering topics related to Sequence assembly, Genomics, Microbiology + button_link: + https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html + button_tip: View tutorial + button_icon: tutorial - title_md: Checking expected species and contamination in bacterial isolate description_md: Tutorial stored in Ecology topic on the Galaxy Training Network and covering topics related to Whole genome sequencing, Genomics, Microbiology, @@ -538,20 +552,19 @@ tabs: https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Genome annotation with Prokka - description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training - Network and covering topics related to Genomics, Microbiology, Gene and protein - families, Sequence analysis + - title_md: Phylogenetic analysis for bacterial comparative genomics + description_md: Tutorial stored in Evolution topic on the Galaxy Training Network + and covering topics related to Genomics, Microbiology, Phylogeny button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html + https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Refining Genome Annotations with Apollo (prokaryotes) + - title_md: Genome annotation with Prokka description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Microbiology, Gene and protein families, Sequence analysis button_link: - https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Bacterial Genome Annotation @@ -572,10 +585,32 @@ tabs: https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html button_tip: View tutorial button_icon: tutorial + - title_md: Refining Genome Annotations with Apollo (prokaryotes) + description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training + Network and covering topics related to Genomics, Microbiology, Gene and protein + families, Sequence analysis + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html + button_tip: View tutorial + button_icon: tutorial + - title_md: Bacterial genome quality control + description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training + Network and covering topics related to Genomics, Microbiology + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html + button_tip: View tutorial + button_icon: tutorial + - title_md: Dataset construction for bacterial comparative genomics + description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training + Network and covering topics related to Genomics, Microbiology + button_link: + https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html + button_tip: View tutorial + button_icon: tutorial - title_md: Comparative gene analysis in unannotated genomes description_md: Tutorial stored in Genome Annotation topic on the Galaxy Training Network and covering topics related to Genomics, Gene and protein families, - Sequence analysis, Phylogeny + Sequence analysis, Phylogeny, Comparative genomics button_link: https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html button_tip: View tutorial @@ -604,19 +639,19 @@ tabs: https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 2: Function' + - title_md: 'metaQuantome 1: Data creation' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network - and covering topics related to Proteomics, Proteogenomics, Metatranscriptomics, - Microbial ecology, Metagenomics + and covering topics related to Proteomics, Proteogenomics, Biodiversity, Taxonomy button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 1: Data creation' + - title_md: 'metaQuantome 3: Taxonomy' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network - and covering topics related to Proteomics, Proteogenomics, Biodiversity, Taxonomy + and covering topics related to Proteomics, Proteogenomics, Metatranscriptomics, + Microbial ecology, Metagenomics, Taxonomy button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Metaproteomics tutorial @@ -626,12 +661,12 @@ tabs: https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 'metaQuantome 3: Taxonomy' + - title_md: 'metaQuantome 2: Function' description_md: Tutorial stored in Proteomics topic on the Galaxy Training Network and covering topics related to Proteomics, Proteogenomics, Metatranscriptomics, - Microbial ecology, Metagenomics, Taxonomy + Microbial ecology, Metagenomics button_link: - https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html + https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Quality and contamination control in bacterial isolate using Illumina @@ -651,27 +686,36 @@ tabs: https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html button_tip: View tutorial button_icon: tutorial - - id: learning-pathway title: Learning pathways - heading_md: > - Connected tutorials to train you to perform microbial isolates data analysis. + heading_md: "Connected tutorials to train you to perform microbial isolates data + analysis.\n" content: - - title_md: Detection of AMR genes in bacterial genomes - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of bacterial genomics data. You will learn how to use Galaxy for analysis and will be guided through the common steps of bacterial genomics analysis: species and contamination checking, assembly, genome annotation, and AMR gene detection. - button_link: https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html - button_icon: tutorial - button_tip: Open Learning Pathway - - title_md: Proteogenomics - description_md: > - This learning path aims to teach you the analysis of proteogenomics data. You will learn how to use Galaxy for analysis and will be guided through the common steps of proteogenomics analysis: database generation, database searching, and novel peptide analysis. - button_link: https://training.galaxyproject.org/training-material/learning-pathways/proteogenomics.html - button_icon: tutorial - button_tip: Open Learning Pathway - - title_md: Genome annotation for prokaryotes - description_md: > - This learning path aims to teach you the genome annotation for prokaryotes. You will learn how to use Galaxy for analysis and will be guided through the common steps of genome annotation for prokaryotes: introduction to genome annotation, gene calling and functional annotation, and manual curation. - button_link: https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html - button_icon: tutorial - button_tip: Open Learning Pathway + - title_md: Detection of AMR genes in bacterial genomes + description_md: "This learning path aims to teach you the basics of Galaxy and + analysis of bacterial genomics data. You will learn how to use Galaxy for analysis + and will be guided through the common steps of bacterial genomics analysis: + species and contamination checking, assembly, genome annotation, and AMR gene + detection.\n" + button_link: + https://training.galaxyproject.org/training-material/learning-pathways/amr-gene-detection.html + button_icon: tutorial + button_tip: Open Learning Pathway + - title_md: Proteogenomics + description_md: "This learning path aims to teach you the analysis of proteogenomics + data. You will learn how to use Galaxy for analysis and will be guided through + the common steps of proteogenomics analysis: database generation, database searching, + and novel peptide analysis.\n" + button_link: + https://training.galaxyproject.org/training-material/learning-pathways/proteogenomics.html + button_icon: tutorial + button_tip: Open Learning Pathway + - title_md: Genome annotation for prokaryotes + description_md: "This learning path aims to teach you the genome annotation for + prokaryotes. You will learn how to use Galaxy for analysis and will be guided + through the common steps of genome annotation for prokaryotes: introduction + to genome annotation, gene calling and functional annotation, and manual curation.\n" + button_link: + https://training.galaxyproject.org/training-material/learning-pathways/genome-annotation-prokaryote.html + button_icon: tutorial + button_tip: Open Learning Pathway diff --git a/communities/microgalaxy/lab/sections/3_microbiome.yml b/communities/microgalaxy/lab/sections/3_microbiome.yml index 023e0912e..a48696cfb 100644 --- a/communities/microgalaxy/lab/sections/3_microbiome.yml +++ b/communities/microgalaxy/lab/sections/3_microbiome.yml @@ -3,516 +3,543 @@ title: Microbiome tabs: - id: overview title: Overview - heading_md: > - Microbiome data analysis can encompass metabarcoding, metagenomics, metatranscriptomics, and metaproteomics. These analyses (from raw data to differential analyses or visualization via assembly) are supported in microGalaxy with different tool suites and potential analyses available on microGalaxy. + heading_md: "Microbiome data analysis can encompass metabarcoding, metagenomics, + metatranscriptomics, and metaproteomics. These analyses (from raw data to differential + analyses or visualization via assembly) are supported in microGalaxy with different + tool suites and potential analyses available on microGalaxy. \n" content: - - title_md: "Overview of possible microbiome data analysis tasks with corresponding tool suites" - description_md: | -
- Overview of microbial data analysis -

- - Outputs are color-coded by type and numbers indicate available tool suites for each step. - - Input data (blue) represent raw datasets, including sequencing reads and mass spectra. - Intermediate outputs (gray) include cleaned reads, assemblies, and OTUs/AVSs. - Taxonomic outputs (green) represent taxonomic profiling results. - Functional outputs (yellow) highlight functional profiling and differential feature analysis. - Other outputs (orange) indicate annotated genomes, reconstructed genomes, and antibiotic resistance genes. - - Numbers correspond to tool suites: - (1) FastQC, - Cutadapt, - fastp, - MultiQC, - Porechop, - Filtlong, - NanoPlot, - SortMeRNA, - Bowtie, - minimap - - (2) MetaPhlAn, - Kraken2, - Bracken, - Diamond, - [soon] Sylph, - mOTUs, - (Re)Centrifuge, - GTDB-Tk - - (4) Bakta, - Prokka, - Prodigal, - braker, - eggNOG Mapper, - InterProScan - - (5) HMMER - - (6) Bakta, - AMRFinderPlus, - ABRicate, - fARGene, - hAMRonization, - argNorm, - StarAMR, - TB-Profiler - - (7) ABRicate - - (8) ISEScan, - Transit, - PlasmidFinder - - (9) StarAMR, - chewBBaca (e.g. chewBBaca create schema), - pyMLST (e.g. Add strain to cg/wgMLST database), - MLST, - SISTR - - (10) CRISPRCasFinder - - (11) antiSMASH, - HMMER - - (12) Gene Ontology, - KEGG - - (21) msconvert, - OpenMS (e.g. XTandemAdapter) - - (22) SearchGUI, - PeptideShaker, - MaxQuant, - FragPipe - - (23) MaxQuant, - PepQuery, - FragPipe, - MSstatsTMT, - iTRAQ, - UniPept - - (24) MSStats - - (25) QIIME2 (e.g. qiime2 diversity alpha), - dada2 (e.g. dada2 dada), - LotuS2, - Mothur, - Phyloseq, - mOTUs, - FROGS (e.g. FROGS Affiliation OTU) - - (26) PICRUSt2 (e.g. PICRUSt2 Metagenome prediction) - - (27) MaAsLin2, - edgeR, - ANCOM, - ALDEx2 - - (28) Krakentools (e.g. Krakentools Calculates alpha diversity) - - (29) KRONA, - GraPhlAn, - Pavian, - Phinch - - (30) HUMAnN, - minimap, - BWA-MEM, - Diamond - - (31) Groot, - deepARG - - (32) MEGAHIT, - MetaSPades, - Flye, - Unicycler, - Racon, - Pilon, - Polypolish, - (meta)QUAST - - (33) MetaBAT, - concoct, - MAxBin, - SemiBin (e.g. SemiBin), - DASTool, - dRep (e.g. dRep compare), - CoverM (e.g. CoverM contig), - CheckM (e.g. CheckM analyze), - VirSorter, - Binette - - (34) GTDB-Tk, - Contig Annotation Tool (CAT) (e.g. GTDB-Tk) - - (35) MetaNovo - - (36) Unipept - - (37) MetaQuantome - -

- Note: If a tool link does not work or is missing, it may not be installed on this server. Please contact - support for assistance. - If a tool is not listed here and you cannot find it in the tool's panel, you can request it via the microGalaxy community: - microgalaxy@lists.galaxyproject.org. -

-
- + - title_md: Overview of possible microbiome data analysis tasks with corresponding + tool suites + description_md: "
\n \"Overview\n

\n\n Outputs are color-coded by type and numbers indicate available + tool suites for each step.\n\n Input data (blue) represent + raw datasets, including sequencing reads and mass spectra. \n Intermediate + outputs (gray) include cleaned reads, assemblies, and OTUs/AVSs. \n\ + \ Taxonomic outputs (green) represent taxonomic profiling + results. \n Functional outputs (yellow) highlight functional + profiling and differential feature analysis. \n Other outputs (orange) + indicate annotated genomes, reconstructed genomes, and antibiotic resistance + genes.\n\n Numbers correspond to tool suites: \ + \ \n (1) FastQC, \n Cutadapt, \n fastp, \n MultiQC,\n Porechop, \n Filtlong, \n NanoPlot, \n SortMeRNA, \n Bowtie, \n minimap \n\n (2) MetaPhlAn, \n Kraken2, \n Bracken, \n Diamond, \n [soon] Sylph, \n mOTUs, \n (Re)Centrifuge, \n GTDB-Tk\n\n (4) Bakta, \n Prokka, \n Prodigal, \n braker,\n eggNOG Mapper,\n InterProScan \n\n (5) HMMER \n\n (6) Bakta, \n AMRFinderPlus, \n ABRicate, \n fARGene, \n hAMRonization,\n argNorm, \n StarAMR, \n TB-Profiler\n\n (7) ABRicate\n\n (8) ISEScan, \n Transit, \n PlasmidFinder\n\n (9) StarAMR, \n chewBBaca (e.g. chewBBaca create schema), \n pyMLST (e.g. Add strain to cg/wgMLST database), \n MLST, \n SISTR \n\n (10) CRISPRCasFinder \n\n (11) antiSMASH, \n HMMER \n\n (12) Gene Ontology, \n KEGG\n\n (21) msconvert, \n OpenMS (e.g. XTandemAdapter)\n\n (22) SearchGUI,\n PeptideShaker,\n MaxQuant,\n FragPipe\n\n (23) MaxQuant,\n PepQuery,\n FragPipe,\n MSstatsTMT,\n iTRAQ,\n UniPept \n\n (24) MSStats \n\n (25) QIIME2 (e.g. qiime2 diversity alpha), \n dada2 (e.g. dada2 dada), \n LotuS2, \n Mothur,\n Phyloseq, + \n mOTUs, \n FROGS (e.g. FROGS Affiliation OTU)\n\n (26) PICRUSt2 (e.g. PICRUSt2 Metagenome prediction)\n\n (27) MaAsLin2, \n edgeR, \n ANCOM, \n ALDEx2 \n\n (28) Krakentools (e.g. Krakentools Calculates alpha diversity)\n\n (29) + KRONA, \n GraPhlAn, \n Pavian, \n Phinch \n\n (30) HUMAnN, \n minimap, \n BWA-MEM, \n Diamond \n\n (31) Groot, \n deepARG \n\n (32) MEGAHIT, \n MetaSPades, \n Flye, \n Unicycler, \n Racon, \n Pilon, \n Polypolish, \n (meta)QUAST \n\n (33) MetaBAT, \n concoct, \n MAxBin, \n SemiBin (e.g. SemiBin), \n DASTool, \n dRep (e.g. dRep compare), \n CoverM (e.g. CoverM contig), \n CheckM (e.g. CheckM analyze),\n VirSorter, \n Binette\n\n (34) GTDB-Tk,\n Contig Annotation Tool (CAT) (e.g. GTDB-Tk)\n \n (35) MetaNovo \n\n (36) Unipept \n\n (37) MetaQuantome\n \n

\n Note: + If a tool link does not work or is missing, it may not be installed on this + server. Please contact \n support for assistance.\ + \ \n If a tool is not listed here and you cannot find it in the tool's panel, + you can request it via the microGalaxy community: \n microgalaxy@lists.galaxyproject.org.\n

\n
\n" - id: tools title: Tools - heading_md: > - Flagship tools for microbiome analysis + heading_md: "Flagship tools for microbiome analysis\n" content: subsections: - - id: metabarcoding - title: Metabarcoding - content: - - title_md: QIIME2 Beta Diversity - Microbiome Analysis with QIIME2 - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta" - description_md: Computes a user-specified phylogenetic beta diversity metric for all pairs of samples in a feature table. - - title_md: LotuS2 - fast OTU processing pipeline - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2" - description_md: An ultrafast and highly accurate tool for amplicon sequencing analysis. - - title_md: dada2 - Accurate, high-resolution sample inference from amplicon sequencing data - description_md: > - The dada2 infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. - - - title_md: PICRUSt2 - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States - description_md: > - PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. - - - id: metagenomics - title: Metagenomics - content: - - title_md: Kraken2 - Taxonomic profiler - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken2%2Fkraken2" - description_md: > - Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. - - title_md: Krona - Visualization of taxonomic profiles - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart" - description_md: > - Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. - - title_md: MEGAHIT - An ultra-fast and memory-efficient short-read assembler - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit" - description_md: > - An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. - - title_md: MetaBAT2 - An adaptive binning algorithm for genome reconstruction from metagenome assemblies - 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: CONCOCT - A program for unsupervised binning of metagenomic contigs - 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: CheckM - A set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes - description_md: > - Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes - - - id: metatranscriptomics - title: Metatranscriptomics - content: - - title_md: MetaPhlAn - A tool to profile the composition of microbial communities - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan" - description_md: > - A computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics. For details on StrainPhlAn, visit its dedicated . - - title_md: HUMAnN - profile presence/absence and abundance of microbial pathways and gene families - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann" - description_md: > - HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data. - - id: metaproteomics - title: Metaproteomics - content: - - title_md: msconvert - A tool for converting and/or filtering mass spectrometry files - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert" - description_md: > - A tool to convert between various file formats, such as mzML, mz5, mgf, text, ms1, cms1, ms2, cms2, with many options. - - title_md: MaxQuant - A tool for analyzing large mass-spectrometric - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant" - description_md: > - MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. - - title_md: OpenMS - A framework for Mass Spectrometry - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter" - description_md: > - OpenMS offers a C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. It empowers rapid development of mass spectrometry related software. - - title_md: Metanovo - A pipeline for probabilistic peptide discovery in complex metaproteomic datasets - button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo" - description_md: > - MetaNovo is a pipeline that integrates existing tools with a custom algorithm to produce targeted protein sequence databases for mass spectrometry metaproteomic analysis as an intermediate filtering step prior to standard sequence database search approaches. - + - id: metabarcoding + title: Metabarcoding + content: + - title_md: QIIME2 Beta Diversity - Microbiome Analysis with QIIME2 + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta' + description_md: Computes a user-specified phylogenetic beta diversity metric + for all pairs of samples in a feature table. + - title_md: LotuS2 - fast OTU processing pipeline + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2' + description_md: An ultrafast and highly accurate tool for amplicon sequencing + analysis. + - title_md: dada2 - Accurate, high-resolution sample inference + from amplicon sequencing data + description_md: "The dada2 infers exact amplicon sequence variants (ASVs) + from high-throughput amplicon sequencing data, replacing the coarser and + less accurate OTU clustering approach. \n" + - title_md: PICRUSt2 - Phylogenetic Investigation of Communities + by Reconstruction of Unobserved States + description_md: "PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States) is a software for predicting functional abundances + based only on marker gene sequences. \n" + - id: metagenomics + title: Metagenomics + content: + - title_md: Kraken2 - Taxonomic profiler + button_link: '{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fkraken2%2Fkraken2' + description_md: "Kraken 2 is the newest version of Kraken, a taxonomic classification + system using exact k-mer matches to achieve high accuracy and fast classification + speeds. \n" + - title_md: Krona - Visualization of taxonomic profiles + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart' + description_md: "Krona allows hierarchical data to be explored with zooming, + multi-layered pie charts. \n" + - title_md: MEGAHIT - An ultra-fast and memory-efficient short-read + assembler + button_link: '{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit' + description_md: "An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph.\n" + - title_md: MetaBAT2 - An adaptive binning algorithm for genome + reconstruction from metagenome assemblies + 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. + \n" + - title_md: CONCOCT - A program for unsupervised binning of metagenomic + contigs + 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. \n" + - title_md: CheckM - A set of tools for assessing the quality of + genomes recovered from isolates, single cells, or metagenomes + description_md: "Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes \n" + - id: metatranscriptomics + title: Metatranscriptomics + content: + - title_md: MetaPhlAn - A tool to profile the composition of microbial + communities + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan' + description_md: "A computational tool for species-level microbial profiling + (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing + data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial + population genomics. For details on StrainPhlAn, visit its dedicated .\n" + - title_md: HUMAnN - profile presence/absence and abundance of + microbial pathways and gene families + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann' + description_md: "HUMAnN is a method for efficiently and accurately profiling + the abundance of microbial metabolic pathways and other molecular functions + from metagenomic or metatranscriptomic sequencing data.\n" + - id: metaproteomics + title: Metaproteomics + content: + - title_md: msconvert - A tool for converting and/or filtering + mass spectrometry files + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert' + description_md: "A tool to convert between various file formats, such as mzML, + mz5, mgf, text, ms1, cms1, ms2, cms2, with many options.\n" + - title_md: MaxQuant - A tool for analyzing large mass-spectrometric + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant' + description_md: "MaxQuant is a quantitative proteomics software package designed + for analyzing large mass-spectrometric data sets. It is specifically aimed + at high-resolution MS data.\n" + - title_md: OpenMS - A framework for Mass Spectrometry + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter' + description_md: "OpenMS offers a C++ library (+ Python bindings) for LC/MS + data management, analysis and visualization. It empowers rapid development + of mass spectrometry related software.\n" + - title_md: Metanovo - A pipeline for probabilistic peptide discovery + in complex metaproteomic datasets + button_link: '{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo' + description_md: "MetaNovo is a pipeline that integrates existing tools with + a custom algorithm to produce targeted protein sequence databases for mass + spectrometry metaproteomic analysis as an intermediate filtering step prior + to standard sequence database search approaches.\n" - id: interactive-tools title: Interactive tools - heading_md: > - Interactive tools for microbial research + heading_md: "Interactive tools for microbial research \n" content: - - title_md: Phyloseq - Explore microbiome profiles - description_md: > - The phyloseq package is a tool to import, store, analyze, and graphically display complex phylogenetic sequencing data that has already been clustered into Operational Taxonomic Units (OTUs), especially when there is associated sample data, phylogenetic tree, and/or taxonomic assignment of the OTUs. - inputs: - - datatypes: - - phyloseq R object - button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_phyloseq" - - title_md: Pavian - Interactive analysis of metagenomics data - description_md: > - An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome. - inputs: - - datatypes: - - Kraken report - - MetaPhlAn report - button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian" - - title_md: Phinch - A framework for visualizing bio data - description_md: > - Interactive tool for visualising Biom data. - inputs: - - datatypes: - - Biom - button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_phinch" - + - title_md: Phyloseq - Explore microbiome profiles + description_md: "The phyloseq package is a tool to import, store, analyze, and + graphically display complex phylogenetic sequencing data that has already been + clustered into Operational Taxonomic Units (OTUs), especially when there is + associated sample data, phylogenetic tree, and/or taxonomic assignment of the + OTUs.\n" + inputs: + - datatypes: + - phyloseq R object + button_link: '{{ galaxy_base_url }}/root?tool_id=interactive_tool_phyloseq' + - title_md: Pavian - Interactive analysis of metagenomics data + description_md: "An interactive browser application for analyzing and visualization + metagenomics classification results from classifiers such as Kraken, KrakenUniq, + Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer + for validation of matches to a particular genome.\n" + inputs: + - datatypes: + - Kraken report + - MetaPhlAn report + button_link: '{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian' + - title_md: Phinch - A framework for visualizing bio data + description_md: "Interactive tool for visualising Biom data.\n" + inputs: + - datatypes: + - Biom + button_link: '{{ galaxy_base_url }}/root?tool_id=interactive_tool_phinch' - id: databases title: Databases - heading_md: Examples of databases prebuilt in some tools by microGalaxy. Even more databases are also found in microGalaxy, such as PhageDB, MAdLandDB, SwissProt, PDB, etc. + heading_md: Examples of databases prebuilt in some tools by microGalaxy. Even more + databases are also found in microGalaxy, such as PhageDB, MAdLandDB, SwissProt, + PDB, etc. content: subsections: - - id: taxonomic-classification - title: Taxonomic Classification Databases - content: - - title_md: RefSeq - Reference Sequence Database - button_link: "https://www.ncbi.nlm.nih.gov/refseq/" - button_tip: "Visit RefSeq" - description_md: > - A high-quality reference database of curated genomic sequences from NCBI. - Used in tools such as [Kraken2]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2) and [BLAST]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info) - - title_md: SILVA - 16S/18S/28S rRNA gene reference database - button_link: "https://www.arb-silva.de/" - button_tip: "Visit SILVA" - description_md: > - SILVA provides high-quality reference sequences for rRNA-based microbial classification. - Used in tools such as [LotuS2]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2), [dada2: assignTaxonomy and addSpecies]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies), [Kraken2]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2), Mothur and QIIME - - title_md: Greengenes - 16S rRNA reference database - button_link: "https://greengenes.secondgenome.com/" - button_tip: "Visit Greengenes" - description_md: > - A widely used 16S rRNA gene reference for microbial classification. - Used in tools such as [dada2: assignTaxonomy and addSpecies]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies) - - title_md: GTDB - Genome Taxonomy Database - button_link: "https://gtdb.ecogenomic.org/" - button_tip: "Visit GTDB" - description_md: > - A curated genome-based taxonomy database for bacteria and archaea. - Used in tools such as [GTDB-Tk]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf) and [dada2: assignTaxonomy and addSpecies]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies) - - title_md: ChocoPhlAn (MetaPhlAn) - Marker gene database for metagenomic profiling - button_link: "https://bitbucket.org/biobakery/metaphlan/src/master/" - button_tip: "Visit MetaPhlAn" - description_md: > - ChocoPhlAn is the core marker gene database used by MetaPhlAn for microbial community profiling. - Used in tools such as [MetaPhlAn]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan) and [HUMAnN]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann) - - - id: functional-annotation - title: Functional Annotation Databases - content: - - title_md: KEGG - Kyoto Encyclopedia of Genes and Genomes - button_link: "https://www.kegg.jp/" - button_tip: "Visit KEGG" - description_md: > - A comprehensive database of molecular interactions, reactions, and pathways. - Used in tools such as [KofamScan]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kofamscan/kofamscan) - - title_md: eggNOG - Orthologous gene groups database - button_link: "http://eggnog5.embl.de/" - button_tip: "Visit eggNOG" - description_md: > - A hierarchical database of orthologous gene families and functional annotation. - Used in tools such as [eggNOG-mapper]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper) - - title_md: MetaCyc - Metabolic pathways database - button_link: "https://metacyc.org/" - button_tip: "Visit MetaCyc" - description_md: > - A curated database of metabolic pathways and enzymes from all domains of life. - Used in tools such as Pathway Tools e.g. [KOBAS Identify]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_identify) - - title_md: Gene Ontology (GO) - Functional Gene Annotations - button_link: "http://geneontology.org/" - button_tip: "Visit Gene Ontology" - description_md: > - A database that classifies gene functions and biological processes. - Used in tools such as [GOseq]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq) - - title_md: UniRef - Clustered UniProt Sequences - button_link: "https://www.uniprot.org/uniref/" - button_tip: "Visit UniRef" - description_md: > - A protein sequence database derived from UniProt. - Used in tools such as [HUMAnN]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann) - - - id: resistome - title: Antibiotic Resistance Databases - content: - - title_md: CARD - Comprehensive Antibiotic Resistance Database - button_link: "https://card.mcmaster.ca/" - button_tip: "Visit CARD" - description_md: > - A manually curated reference database of antimicrobial resistance genes. - Used in tools such as [pharokka]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pharokka/pharokka) - - title_md: ResFinder - Identifies acquired antimicrobial resistance genes - button_link: "https://cge.food.dtu.dk/services/ResFinder/" - button_tip: "Visit ResFinder" - description_md: > - A tool for detecting antimicrobial resistance genes in bacterial genomes. - Used in tools such as [ABRicate]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate) and [StarAMR]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search) - - title_md: AMRFinderPlus - Antimicrobial Resistance Database - button_link: "https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/" - button_tip: "Visit AMRFinderPlus" - description_md: > - A curated database for detecting antimicrobial resistance genes. - Used in tools such as [AMRFinderPlus]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus) - - - id: viral-databases - title: Viral Databases - content: - - title_md: IMG/VR - Integrated Microbial Genomes & Virome - button_link: "https://img.jgi.doe.gov/vr/" - button_tip: "Visit IMG/VR" - description_md: > - A comprehensive resource for viral and phage genomes. - Used in tools such as [VirSorter]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/ufz/virsorter/virsorter) - - - id: general-sequence-databases - title: General Sequence Databases - content: - - title_md: NCBI nt - Nucleotide Sequence Database - button_link: "https://www.ncbi.nlm.nih.gov/nucleotide/" - button_tip: "Visit NCBI nt" - description_md: > - The NCBI nucleotide (nt) database is a comprehensive collection of nucleotide sequences from GenBank, RefSeq, and other sources. - Used in tools such as [BLASTn]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper) - - - title_md: NCBI nr - Non-Redundant Protein Database - button_link: "https://www.ncbi.nlm.nih.gov/protein/" - button_tip: "Visit NCBI nr" - description_md: > - The NCBI protein (nr) database is a curated non-redundant protein sequence database, integrating data from multiple sources. - Used in tools such as [BLASTp]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper) - - - id: metagenomics - title: Metagenomic Databases - content: - - title_md: MGnify - EBI Metagenomics Database - button_link: "https://www.ebi.ac.uk/metagenomics/" - button_tip: "Visit MGnify" - description_md: > - A collection of metagenomic analyses and annotations from environmental and host-associated samples. - Used in tools such as [Interactive MGnify Notebook]({{ galaxy_base_url }}/root?tool_id=interactive_tool_mgnify_notebook) - + - id: taxonomic-classification + title: Taxonomic Classification Databases + content: + - title_md: RefSeq - Reference Sequence Database + button_link: https://www.ncbi.nlm.nih.gov/refseq/ + button_tip: Visit RefSeq + description_md: "A high-quality reference database of curated genomic sequences + from NCBI. Used in tools such as [Kraken2]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2) and [BLAST]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info)\n" + - title_md: SILVA - 16S/18S/28S rRNA gene reference database + button_link: https://www.arb-silva.de/ + button_tip: Visit SILVA + description_md: "SILVA provides high-quality reference sequences for rRNA-based + microbial classification. Used in tools such as [LotuS2]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2), + [dada2: assignTaxonomy and addSpecies]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies), + [Kraken2]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2), + Mothur and QIIME\n" + - title_md: Greengenes - 16S rRNA reference database + button_link: https://greengenes.secondgenome.com/ + button_tip: Visit Greengenes + description_md: "A widely used 16S rRNA gene reference for microbial classification. + Used in tools such as [dada2: assignTaxonomy and addSpecies]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies)\n" + - title_md: GTDB - Genome Taxonomy Database + button_link: https://gtdb.ecogenomic.org/ + button_tip: Visit GTDB + description_md: "A curated genome-based taxonomy database for bacteria and + archaea. Used in tools such as [GTDB-Tk]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf) + and [dada2: assignTaxonomy and addSpecies]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies)\n" + - title_md: ChocoPhlAn (MetaPhlAn) - Marker gene database for metagenomic + profiling + button_link: https://bitbucket.org/biobakery/metaphlan/src/master/ + button_tip: Visit MetaPhlAn + description_md: "ChocoPhlAn is the core marker gene database used by MetaPhlAn + for microbial community profiling. Used in tools such as [MetaPhlAn]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan) + and [HUMAnN]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann)\n" + - id: functional-annotation + title: Functional Annotation Databases + content: + - title_md: KEGG - Kyoto Encyclopedia of Genes and Genomes + button_link: https://www.kegg.jp/ + button_tip: Visit KEGG + description_md: "A comprehensive database of molecular interactions, reactions, + and pathways. Used in tools such as [KofamScan]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kofamscan/kofamscan)\n" + - title_md: eggNOG - Orthologous gene groups database + button_link: http://eggnog5.embl.de/ + button_tip: Visit eggNOG + description_md: "A hierarchical database of orthologous gene families and + functional annotation. Used in tools such as [eggNOG-mapper]({{ + galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper)\n" + - title_md: MetaCyc - Metabolic pathways database + button_link: https://metacyc.org/ + button_tip: Visit MetaCyc + description_md: "A curated database of metabolic pathways and enzymes from + all domains of life. Used in tools such as Pathway Tools e.g. [KOBAS + Identify]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_identify)\n" + - title_md: Gene Ontology (GO) - Functional Gene Annotations + button_link: http://geneontology.org/ + button_tip: Visit Gene Ontology + description_md: "A database that classifies gene functions and biological + processes. Used in tools such as [GOseq]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq)\n" + - title_md: UniRef - Clustered UniProt Sequences + button_link: https://www.uniprot.org/uniref/ + button_tip: Visit UniRef + description_md: "A protein sequence database derived from UniProt. Used in + tools such as [HUMAnN]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/humann/humann)\n" + - id: resistome + title: Antibiotic Resistance Databases + content: + - title_md: CARD - Comprehensive Antibiotic Resistance Database + button_link: https://card.mcmaster.ca/ + button_tip: Visit CARD + description_md: "A manually curated reference database of antimicrobial resistance + genes. Used in tools such as [pharokka]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pharokka/pharokka)\n" + - title_md: ResFinder - Identifies acquired antimicrobial resistance + genes + button_link: https://cge.food.dtu.dk/services/ResFinder/ + button_tip: Visit ResFinder + description_md: "A tool for detecting antimicrobial resistance genes in bacterial + genomes. Used in tools such as [ABRicate]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate) and + [StarAMR]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search)\n" + - title_md: AMRFinderPlus - Antimicrobial Resistance Database + button_link: https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/ + button_tip: Visit AMRFinderPlus + description_md: "A curated database for detecting antimicrobial resistance + genes. Used in tools such as [AMRFinderPlus]({{ galaxy_base_url + }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus)\n" + - id: viral-databases + title: Viral Databases + content: + - title_md: IMG/VR - Integrated Microbial Genomes & Virome + button_link: https://img.jgi.doe.gov/vr/ + button_tip: Visit IMG/VR + description_md: "A comprehensive resource for viral and phage genomes. Used + in tools such as [VirSorter]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/ufz/virsorter/virsorter)\n" + - id: general-sequence-databases + title: General Sequence Databases + content: + - title_md: NCBI nt - Nucleotide Sequence Database + button_link: https://www.ncbi.nlm.nih.gov/nucleotide/ + button_tip: Visit NCBI nt + description_md: "The NCBI nucleotide (nt) database is a comprehensive collection + of nucleotide sequences from GenBank, RefSeq, and other sources. Used in + tools such as [BLASTn]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper)\n" + - title_md: NCBI nr - Non-Redundant Protein Database + button_link: https://www.ncbi.nlm.nih.gov/protein/ + button_tip: Visit NCBI nr + description_md: "The NCBI protein (nr) database is a curated non-redundant + protein sequence database, integrating data from multiple sources. Used + in tools such as [BLASTp]({{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper)\n" + - id: metagenomics + title: Metagenomic Databases + content: + - title_md: MGnify - EBI Metagenomics Database + button_link: https://www.ebi.ac.uk/metagenomics/ + button_tip: Visit MGnify + description_md: "A collection of metagenomic analyses and annotations from + environmental and host-associated samples. Used in tools such as [Interactive + MGnify Notebook]({{ galaxy_base_url }}/root?tool_id=interactive_tool_mgnify_notebook)\n" - id: workflows title: Workflows - heading_md: Microbiome analysis workflows to use directly, modify or take ideas from + heading_md: Microbiome analysis workflows to use directly, modify or take ideas + from content: subsections: - - id: metabarcoding - title: Metabarcoding Workflows - content: - - title_md: Building an amplicon sequence variant (ASV) table from 16S data using - DADA2 - description_md: Workflow covering operations related to Deposition, Variant calling, - Analysis, Visualisation, and DNA barcoding - button_link: https://dev.workflowhub.eu/workflows/1105?version=2 - button_tip: View workflow - button_icon: view - - title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' - description_md: Workflow covering operations related to Sequence composition calculation, - Validation, Visualisation, Sequence contamination filtering, Taxonomic classification, - Statistical calculation, and Sequencing quality control - button_link: https://dev.workflowhub.eu/workflows/1064?version=1 - button_tip: View workflow - button_icon: view - - - id: metagenomics - title: Metagenomics Workflows - content: - - title_md: Taxonomy classification using Kraken2 and Bracken - description_md: Workflow covering operations related to Visualisation, Taxonomic - classification, Aggregation, Statistical calculationon topics related to Metagenomics, and - Taxonomy - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1199" - button_tip: Import workflow - button_icon: run - - title_md: Analyses of shotgun metagenomics data with MetaPhlAn2 - description_md: Workflow covering operations related to Visualisation, Phylogenetic - tree analysis, Nucleic acid sequence analysison topics related to Metagenomic - sequencing, and Metagenomics - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=624" - button_tip: Import workflow - button_icon: run - - - id: metaproteomics - title: Metaproteomics Workflows - content: - - title_md: 'Clinical Metaproteomics Quantification' - description_md: This workflow perform clinical metaproteomics quantification using MaxQuant. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1177" - button_tip: Import workflow - button_icon: run - - title_md: 'Clinical Metaproteomics Database Generation' - description_md: The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1216" - button_tip: Import workflow - button_icon: run - - title_md: 'Clinical Metaproteomics Data Verification' - description_md: In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1218" - button_tip: Import workflow - button_icon: run - - title_md: 'Clinical Metaproteomics Data Interpretation' - description_md: This workflow perform taxonomic and functional annotations using Unipept and statistical analysis using MSstatsTMT. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1219" - button_tip: Import workflow - button_icon: run - - title_md: 'Clinical Metaproteomics Discovery' - description_md: Workflow for clinical metaproteomics database searching. - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1225" - button_tip: Import workflow - button_icon: run - + - id: metabarcoding + title: Metabarcoding Workflows + content: + - title_md: Building an amplicon sequence variant (ASV) table from 16S data + using DADA2 + description_md: Workflow covering operations related to Deposition, Variant + calling, Analysis, Visualisation, and DNA barcoding + button_link: https://dev.workflowhub.eu/workflows/1105?version=2 + button_tip: View workflow + button_icon: view + - title_md: 'Training: 16S rRNA Analysis with Nanopore Sequencing Reads' + description_md: Workflow covering operations related to Sequence composition + calculation, Validation, Visualisation, Sequence contamination filtering, + Taxonomic classification, Statistical calculation, and Sequencing quality + control + button_link: https://dev.workflowhub.eu/workflows/1064?version=1 + button_tip: View workflow + button_icon: view + - id: metagenomics + title: Metagenomics Workflows + content: + - title_md: Taxonomy classification using Kraken2 and Bracken + description_md: Workflow covering operations related to Visualisation, Taxonomic + classification, Aggregation, Statistical calculationon topics related to + Metagenomics, and Taxonomy + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1199' + button_tip: Import workflow + button_icon: run + - title_md: Analyses of shotgun metagenomics data with MetaPhlAn2 + description_md: Workflow covering operations related to Visualisation, Phylogenetic + tree analysis, Nucleic acid sequence analysison topics related to Metagenomic + sequencing, and Metagenomics + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=624' + button_tip: Import workflow + button_icon: run + - id: metaproteomics + title: Metaproteomics Workflows + content: + - title_md: Clinical Metaproteomics Quantification + description_md: This workflow perform clinical metaproteomics quantification + using MaxQuant. + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1177' + button_tip: Import workflow + button_icon: run + - title_md: Clinical Metaproteomics Database Generation + description_md: The workflow begins with the Database Generation process. + The Galaxy-P team has developed a workflow that collects protein sequences + from known disease-causing microorganisms to build a comprehensive database. + This extensive database is then refined into a smaller, more relevant dataset + using the Metanovo tool. + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1216' + button_tip: Import workflow + button_icon: run + - title_md: Clinical Metaproteomics Data Verification + description_md: In proteomics research, verifying detected peptides is essential + for ensuring data accuracy and biological relevance. This tutorial continues + from the clinical metaproteomics discovery workflow, focusing on verifying + identified microbial peptides using the PepQuery tool. + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1218' + button_tip: Import workflow + button_icon: run + - title_md: Clinical Metaproteomics Data Interpretation + description_md: This workflow perform taxonomic and functional annotations + using Unipept and statistical analysis using MSstatsTMT. + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1219' + button_tip: Import workflow + button_icon: run + - title_md: Clinical Metaproteomics Discovery + description_md: Workflow for clinical metaproteomics database searching. + button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1225' + button_tip: Import workflow + button_icon: run - id: tutorials title: Tutorials heading_md: Tutorials to train you to perform microbiome data analysis @@ -525,14 +552,6 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 16S Microbial analysis with Nanopore data - description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, - Metabarcoding - button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html - button_tip: View tutorial - button_icon: tutorial - title_md: Metatranscriptomics analysis using microbiome RNA-seq data (short) description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metatranscriptomics, Microbial ecology, Taxonomy, @@ -541,19 +560,20 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Assembly of metagenomic sequencing data + - title_md: Metatranscriptomics analysis using microbiome RNA-seq data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Metagenomics, Sequence assembly + and covering topics related to Metatranscriptomics, Microbial ecology, Taxonomy, + Function analysis, Sequence analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Taxonomic Profiling and Visualization of Metagenomic Data + - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network and covering topics related to Metagenomics, Microbial ecology, Taxonomy, Sequence analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Antibiotic resistance detection @@ -565,29 +585,19 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Identification of the micro-organisms in a beer using Nanopore sequencing - description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Metagenomics, Microbial ecology, Taxonomy, Sequence - analysis - button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html - button_tip: View tutorial - button_icon: tutorial - - title_md: Metatranscriptomics analysis using microbiome RNA-seq data + - title_md: 16S Microbial analysis with Nanopore data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Metatranscriptomics, Microbial ecology, Taxonomy, - Function analysis, Sequence analysis + and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, + Metabarcoding button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - - Foodborne Edition + - title_md: Assembly of metagenomic sequencing data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Metagenomics, Public health and epidemiology, - Taxonomy, Sequence assembly, Pathology, Sequence analysis + and covering topics related to Metagenomics, Sequence assembly button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: Building an amplicon sequence variant (ASV) table from 16S data using @@ -599,11 +609,21 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: Binning of metagenomic sequencing data + - title_md: Taxonomic Profiling and Visualization of Metagenomic Data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Metagenomics, Sequence assembly + and covering topics related to Metagenomics, Microbial ecology, Taxonomy, Sequence + analysis button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html + button_tip: View tutorial + button_icon: tutorial + - title_md: Pathogen detection from (direct Nanopore) sequencing data using Galaxy + - Foodborne Edition + description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network + and covering topics related to Metagenomics, Public health and epidemiology, + Taxonomy, Sequence assembly, Pathology, Sequence analysis + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: QIIME 2 Moving Pictures @@ -622,12 +642,11 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html button_tip: View tutorial button_icon: tutorial - - title_md: 16S Microbial Analysis with mothur (short) + - title_md: Binning of metagenomic sequencing data description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network - and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, - Metabarcoding + and covering topics related to Metagenomics, Sequence assembly button_link: - https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html + https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html button_tip: View tutorial button_icon: tutorial - title_md: 16S Microbial Analysis with mothur (extended) @@ -638,21 +657,35 @@ tabs: https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html button_tip: View tutorial button_icon: tutorial - + - title_md: 16S Microbial Analysis with mothur (short) + description_md: Tutorial stored in Microbiome topic on the Galaxy Training Network + and covering topics related to Microbial ecology, Taxonomy, Sequence analysis, + Metabarcoding + button_link: + https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html + button_tip: View tutorial + button_icon: tutorial - id: learning-pathway title: Learning pathways - heading_md: > - Connected tutorials to train you to perform microbial data analysis. + heading_md: "Connected tutorials to train you to perform microbial data analysis.\n" content: - - title_md: Metagenomics data processing and analysis for microbiome - description_md: > - This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications - button_link: https://training.galaxyproject.org/training-material/learning-pathways/metagenomics.html - button_icon: tutorial - button_tip: Open Learning Pathway - - title_md: Clinical metaproteomics workflows within Galaxy - description_md: > - This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis. - button_link: https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html - button_icon: tutorial - button_tip: Open Learning Pathway + - title_md: Metagenomics data processing and analysis for microbiome + description_md: "This learning path aims to teach you the basics of Galaxy and + analysis of metagenomics data. You will learn how to use Galaxy for analysis, + and will be guided through the common steps of microbiome data analysis: quality + control, taxonomic profiling, taxonomic binning, assembly, functional profiling, + and also some applications\n" + button_link: + https://training.galaxyproject.org/training-material/learning-pathways/metagenomics.html + button_icon: tutorial + button_tip: Open Learning Pathway + - title_md: Clinical metaproteomics workflows within Galaxy + description_md: "This learning path aims to teach you the basics of how to perform + metaproteomics analysis of the clinical data within the Galaxy platform. You + will learn how to use Galaxy for analysis and will be guided through the most + common first steps of any metaproteomics database generation to searching the + database, verifying the proteins/peptides, and data analysis.\n" + button_link: + https://training.galaxyproject.org/training-material/learning-pathways/clinical-metaproteomics.html + button_icon: tutorial + button_tip: Open Learning Pathway diff --git a/communities/microgalaxy/lab/sections/4_tools.yml b/communities/microgalaxy/lab/sections/4_tools.yml index 650639be8..4830c1d37 100644 --- a/communities/microgalaxy/lab/sections/4_tools.yml +++ b/communities/microgalaxy/lab/sections/4_tools.yml @@ -1,7 +1,5 @@ id: tools title: Community curated tools -exclude_from: - - usegalaxy.org.au tabs: - id: more_tools title: More tools ! @@ -23,7 +21,7 @@ tabs: - title_md: abricate description_md: |- Mass screening of contigs for antiobiotic resistance genes - (Tool usage: 4634468) + (Tool usage: 1566054)