Topic	Title	Link	EDAM topic	EDAM operation	Creation	Last modification	Version	Tutorial	Slides	Video	Workflows	Tools	Servers with precise tool versions	Servers with tool but different versions	Visitors	Page views	Visit duration
Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance	Sequence composition calculation, Sequencing quality control, Mapping assembly, Statistical calculation, Sequence assembly visualisation, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Cross-assembly, Filtering, Genome assembly, Sequence contamination filtering, Sequencing error detection, Scatter plot plotting, Sequence assembly validation, Visualisation, Read mapping	2021-03-24	2024-11-29	15	True	False	False	True	polypolish, porechop, filtlong, nanoplot, fastp, upload1, CONVERTER_bz2_to_uncompressed, fastqc, quast, flye, bwa_mem2, bandage_image	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr	10641	15925	3.400000
Assembly	Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology	Sequence composition calculation, Sequencing quality control, Statistical calculation, Sequence assembly visualisation, Genome assembly, Sequence contamination filtering, Sequence assembly validation, Visualisation, Read mapping	2021-03-24	2025-11-18	17	True	False	True	True	upload1, falco, shovill, fastqc, quast, fastp, bandage_info, bandage_image	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		10408	15938	3.550000
Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Read pre-processing, Formatting, Primer removal, Sequence file editing, Sequence alignment analysis, Read mapping, Sequence composition calculation, Sequencing quality control, Local alignment, Statistical calculation, Sequence assembly visualisation, Variant calling, Data handling, Sequence trimming, Genome assembly, Sequence contamination filtering, Sequence assembly validation, Visualisation	2025-12-28	2025-12-28	0	True	False	True	True	seqtk_subseq, megahit_contig2fastg, tp_cat, cutadapt, bg_uniq, filter_tabular, megahit, ngsutils_bam_filter, collection_column_join, random_lines1, coverm_contig, fastqc, quast, bowtie2, metaspades, bandage_info, bandage_image, bamtools		UseGalaxy.cz, UseGalaxy.eu	0	0	0.000000
Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence composition calculation, Gene prediction, Genome annotation, Sequencing quality control, Statistical calculation, Validation, Aggregation, Genome assembly, Sequence assembly validation, Coding region prediction, Visualisation	2017-10-11	2025-05-15	24	True	True	False	True	prokka, unicycler, multiqc, fastqc, quast	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3159907	8037359	4.383333
Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence visualisation, Sequence alignment, Mapping, Genome visualisation, Read mapping	2018-06-14	2024-06-24	29	True	False	False	True	join1, Cut1, datamash_ops, upload1, cat1, circos_aln_to_links, tp_replace_in_column, tp_cat, circos_interval_to_tiles, jbrowse, circos, fasta_filter_by_length, tp_sort_header_tool, Grep1, Filter1, fasta_compute_length, lastz_wrapper_2, bedtools_complementbed, collapse_dataset, random_lines1, tp_replace_in_line, bedtools_intersectbed, tp_grep_tool, bedtools_sortbed, tp_sed_tool, mergeCols1, addValue			6786	13038	2.916667
Ecology	Checking expected species and contamination in bacterial isolate	https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Taxonomic classification, Statistical calculation, Cross-assembly, Expression analysis	2024-03-04	2025-12-18	5	True	False	False	True	recentrifuge, upload1, est_abundance, kraken2	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	911	1224	3.316667
Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Antimicrobial resistance prediction, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2022-03-16	2025-05-26	13	True	False	False	True	bcftools_consensus, tb_variant_filter, upload1, tp_easyjoin_tool, snippy, addName, tp_cat, Grep1, clustering_from_distmat, __MERGE_COLLECTION__, collapse_dataset, trimmomatic, tp_replace_in_line, tp_grep_tool, samtools_view, snp_dists, tp_sed_tool, snp_sites, tb_profiler_profile	UseGalaxy.eu		3013	4322	2.616667
Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2025-06-04	12	True	False	False	True	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu		2299	3314	2.483333
Evolution	Phylogenetic analysis for bacterial comparative genomics	https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html	Genomics, Microbiology, Phylogeny	Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences)	2025-03-14	2025-03-14	1	True	False	False	False	upload1, fasttree	Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	GalaxyTrakr	113	135	2.483333
Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Gene prediction, Coding region prediction, Genome visualisation, Genome annotation	2018-03-06	2025-03-19	26	True	True	True	True	prokka, jbrowse	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	3165819	8047097	4.250000
Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance	Genome annotation, Antimicrobial resistance prediction, Genome visualisation, Read mapping	2024-01-23	2025-12-18	10	True	False	True	True	jbrowse, upload1, staramr_search, bakta, bowtie2, tbl2gff3, Grep1	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main)	3611	4969	3.000000
Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2025-05-15	22	True	True	True	True	jbrowse, list_organism, iframe, create_or_update, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	2921839	7238611	5.100000
Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Multilocus sequence typing, Nucleic acid feature detection, Genome visualisation, Sequence motif recognition, Protein feature detection, Genome assembly, Scaffolding, Structural variation detection	2024-02-01	2024-10-15	6	True	False	True	True	tp_replace_in_column, jbrowse, upload1, tp_tail_tool, bakta, plasmidfinder, integron_finder, tbl2gff3, isescan, Grouping1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	6778	9234	2.600000
Genome Annotation	Dataset construction for bacterial comparative genomics	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html	Genomics, Microbiology	Sequence database search, Data handling, Data retrieval	2025-03-14	2025-03-14	1	True	False	False	False	Remove beginning1, bg_uniq, Cut1, upload1, cat1, datasets_download_genome, sort1	UseGalaxy.fr	UseGalaxy.cz	85	103	3.033333
Genome Annotation	Bacterial genome quality control	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html	Genomics, Microbiology	Sequence composition calculation, Genome comparison, Sequencing quality control, Statistical calculation, Sequence assembly validation, Validation	2025-03-14	2025-03-14	1	True	False	False	False	upload1, drep_dereplicate, checkm2	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz	101	111	2.000000
Genome Annotation	Comparative gene analysis in unannotated genomes	https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html	Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics	Database search, Transcriptome assembly, Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis, Coding region prediction, De-novo assembly	2022-09-08	2025-06-03	10	True	False	False	True	regexColumn1, join1, gops_intersect_1, collapse_dataset, bg_diamond_view, Cut1, orfipy, tab2fasta, rapidnj, cat1, bg_diamond, bg_diamond_makedb, tp_split_on_column, Filter1, Add_a_column1, rbc_mafft	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	1885	2636	3.016667
Genome Annotation	Essential genes detection with Transposon insertion sequencing	https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html	Genomics, Microbiology, Sequence analysis, Mobile genetic elements	Transposon prediction, Read pre-processing, Primer removal, Sequence trimming	2019-07-02	2024-03-18	12	True	True	False	True	bg_find_subsequences, transit_gumbel, cutadapt, Cut1, bowtie_wrapper, tp_sort_header_tool, tp_easyjoin_tool, gff_to_prot, __EXTRACT_DATASET__, Filter1, Add_a_column1, deeptools_bam_coverage	UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	3155317	8030191	4.066667
Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation	2018-02-26	2025-03-19	24	True	False	False	True	snippy, jbrowse	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	15311	24422	2.066667
Microbiome	Analyses of metagenomics data - The global picture	https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding	Sequencing quality control, DNA barcoding, Sequence read processing, Sequence clustering, Phylogenetic analysis, Taxonomic classification, Visualisation	2017-06-22	2024-08-09	4	True	False	False	True	mothur_cluster_split, mothur_screen_seqs, mothur_make_shared, mothur_filter_seqs, taxonomy_krona_chart, mothur_align_seqs, mothur_pre_cluster, mothur_make_group, mothur_classify_seqs, mothur_make_biom, metaphlan2, mothur_unique_seqs, metaphlan2krona, humann2_regroup_table, mothur_classify_otu, mothur_count_seqs, krona-text, humann2, mothur_merge_files, mothur_summary_seqs, humann2_renorm_table		UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	9105	12448	2.650000
Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance	Mapping assembly, Sequence assembly visualisation, Antimicrobial resistance prediction, De-novo assembly, Box-Whisker plot plotting, Sequence analysis, Aggregation, Genome assembly, Pairwise sequence alignment, Scatter plot plotting	2019-06-25	2024-06-14	4	True	False	True	True	unicycler, PlasFlow, miniasm, nanoplot, staramr_search, racon, minimap2, gfa_to_fa, bandage_image	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	3327	4651	2.983333
Microbiome	Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition	https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html	Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis	Phylogenetic tree reconstruction, Multiple sequence alignment, Mapping assembly, Base-calling, Antimicrobial resistance prediction, Box-Whisker plot plotting, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Taxonomic classification, Aggregation, Phylogenetic tree generation, Scatter plot plotting, Sequence alignment analysis, Phylogenetic tree generation (from molecular sequences), Sequence composition calculation, Sequencing quality control, Multilocus sequence typing, Sequence assembly, Statistical calculation, Sequence assembly visualisation, Mapping, Variant calling, Data handling, De-novo assembly, Validation, Phylogenetic tree analysis, Genome assembly, Sequence contamination filtering, Pairwise sequence alignment, Cross-assembly, Visualisation	2023-01-26	2025-11-18	12	True	False	True	True	bcftools_consensus, Cut1, abricate, Count1, tab2fasta, tp_cut_tool, samtools_coverage, collection_column_join, medaka_consensus_pipeline, compose_text_param, clustalw, fastp, samtools_fastx, Add_a_column1, __FILTER_FAILED_DATASETS__, tp_replace_in_column, bedtools_getfastabed, clair3, fasttree, newick_display, nanoplot, taxonomy_krona_chart, collection_element_identifiers, fastqc, tp_head_tool, CONVERTER_gz_to_uncompressed, Grep1, tp_find_and_replace, barchart_gnuplot, bamtools_split_mapped, split_file_to_collection, tp_sorted_uniq, bandage_image, param_value_from_file, krakentools_kreport2krona, samtools_depth, Remove beginning1, krakentools_extract_kraken_reads, collapse_dataset, fasta2tab, regex1, ggplot2_heatmap, __BUILD_LIST__, snpSift_extractFields, regexColumn1, multiqc, table_compute, mlst, porechop, add_line_to_file, Paste1, kraken2, __FILTER_EMPTY_DATASETS__, fasta_merge_files_and_filter_unique_sequences, minimap2, flye, tp_split_on_column, tp_multijoin_tool, bcftools_norm, snpSift_filter, Grouping1	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.org.au	4922	7336	3.333333
Microbiome	Taxonomic Profiling and Visualization of Metagenomic Data	https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Genome annotation, Taxonomic classification, Aggregation, Statistical calculation, Visualisation	2023-05-03	2025-12-18	7	True	False	True	True	krakentools_kreport2krona, __UNZIP_COLLECTION__, taxonomy_krona_chart, kraken2, interactive_tool_phinch, interactive_tool_pavian, kraken_biom, est_abundance, metaphlan	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		12542	16743	1.983333
Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Read pre-processing, Formatting, Primer removal, Sequence file editing, Sequence alignment analysis, Read mapping, Sequence composition calculation, Sequencing quality control, Local alignment, Statistical calculation, Sequence assembly visualisation, Variant calling, Data handling, Sequence trimming, Genome assembly, Sequence contamination filtering, Sequence assembly validation, Visualisation	2022-12-05	2025-12-08	8	True	False	True	True	seqtk_subseq, megahit_contig2fastg, tp_cat, cutadapt, bg_uniq, filter_tabular, megahit, ngsutils_bam_filter, collection_column_join, random_lines1, coverm_contig, fastqc, quast, bowtie2, metaspades, bandage_info, bandage_image, bamtools		UseGalaxy.cz, UseGalaxy.eu	4504	6260	2.950000
Microbiome	Building an amplicon sequence variant (ASV) table from 16S data using DADA2	https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding	DNA barcoding, Analysis, Deposition, Variant calling, Visualisation	2024-06-05	2025-07-03	11	True	False	True	True	dada2_makeSequenceTable, cat1, Add_a_column1, __SORTLIST__, tp_replace_in_column, dada2_removeBimeraDenovo, dada2_seqCounts, collection_element_identifiers, tp_head_tool, phyloseq_from_dada2, __UNZIP_COLLECTION__, tp_replace_in_line, dada2_mergePairs, interactive_tool_phyloseq, dada2_plotQualityProfile, dada2_dada, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_filterAndTrim, Grouping1	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		7279	10293	2.366667
Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Sequence composition calculation, Sequencing quality control, Genome annotation, Sequence assembly, Statistical calculation, Sequence clustering, Sequence assembly validation, Validation, Genome comparison, Read binning, Read mapping	2023-12-05	2025-12-02	7	True	False	True	True	checkm_lineage_wf, samtools_sort, concoct_extract_fasta_bins, drep_dereplicate, concoct_cut_up_fasta, concoct, Fasta_to_Contig2Bin, metabat2_jgi_summarize_bam_contig_depths, concoct_coverage_table, maxbin2, bowtie2, metabat2, __BUILD_LIST__, concoct_merge_cut_up_clustering, semibin, das_tool, binette	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main), UseGalaxy.org.au	5744	7029	1.466667
Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding	Sequence composition calculation, Sequencing quality control, Taxonomic classification, Statistical calculation, Sequence contamination filtering, Visualisation, Validation	2020-11-24	2024-07-31	5	True	False	False	True	multiqc, Remove beginning1, porechop, taxonomy_krona_chart, kraken2, fastqc, tp_replace_in_line, datamash_reverse, fastp	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	8451	11665	2.616667
Microbiome	Identification of the micro-organisms in a beer using Nanopore sequencing	https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Sequence composition calculation, Sequencing quality control, Taxonomic classification, Aggregation, Statistical calculation, Visualisation, Sequence contamination filtering	2022-09-29	2024-11-29	5	True	False	True	True	krakentools_kreport2krona, porechop, taxonomy_krona_chart, kraken2, fastqc, fastp, Filter1	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	2791	4076	2.866667
Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Sequence composition calculation, Sequencing quality control, Statistical calculation, Conversion, Phylogenetic tree visualisation, Phylogenetic tree editing, Validation, Sequence alignment analysis, Phylogenetic analysis, Species frequency estimation, Taxonomic classification, Read pre-processing, Sequence trimming, Sequence similarity search, Sequence comparison, Phylogenetic inference, Primer removal, Visualisation	2020-02-13	2025-06-16	6	True	False	True	True	humann_unpack_pathways, Cut1, graphlan, graphlan_annotate, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, taxonomy_krona_chart, tp_sort_header_tool, fastqc, Grep1, tp_find_and_replace, export2graphlan, humann_rename_table, multiqc, cutadapt, fastq_paired_end_interlacer, humann, combine_metaphlan2_humann2, metaphlan, bg_sortmerna	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	815	1068	2.500000
Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification, Aggregation, Primer removal, Sequence alignment analysis, Sequence similarity search, Sequence composition calculation, Sequencing quality control, Statistical calculation, Conversion, Validation, Sequence comparison, Phylogenetic analysis, Species frequency estimation, Sequence trimming, Phylogenetic inference, Visualisation, Read pre-processing	2019-11-21	2025-06-16	6	True	True	True	True	humann_unpack_pathways, Cut1, graphlan, graphlan_annotate, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, taxonomy_krona_chart, tp_sort_header_tool, fastqc, Grep1, tp_find_and_replace, export2graphlan, humann_rename_table, multiqc, cutadapt, fastq_paired_end_interlacer, humann, combine_metaphlan_humann, metaphlan, Grouping1, bg_sortmerna	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.eu	3153894	8024266	4.266667
Microbiome	QIIME 2 Cancer Microbiome Intervention	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding		2024-02-12	2024-03-14	3	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	423	679	3.216667
Microbiome	Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads	https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html	Metagenomics, Sequence assembly	Sequence composition calculation, Genome comparison, Sequencing quality control, Genome annotation, Statistical calculation, Sequence assembly validation, Data handling, Validation	2025-12-18	2025-12-18	1	True	False	False	False	checkm_lineage_wf, join1, tp_replace_in_column, drep_dereplicate, Remove beginning1, multiqc, Cut1, collapse_dataset, fasterq_dump, Summary_Statistics1, tp_sort_header_tool, bakta, collection_column_join, cat1, __EXTRACT_DATASET__, Grouping1	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	19	19	11.283333
Microbiome	QIIME 2 Moving Pictures	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding		2024-03-14	2024-03-14	1	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	606	929	2.633333
Microbiome	16S Microbial Analysis with mothur (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding	Phylogenetic tree reconstruction, Sequencing quality control, DNA barcoding, Sequence read processing, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree generation, Visualisation	2019-05-13	2025-12-18	6	True	False	True	True	mothur_dist_shared, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_make_shared, XY_Plot_1, mothur_heatmap_sim, mothur_filter_seqs, mothur_summary_single, mothur_venn, newick_display, mothur_count_groups, mothur_dist_seqs, mothur_rarefaction_single, mothur_pre_cluster, collapse_dataset, mothur_sub_sample, mothur_remove_seqs, mothur_classify_seqs, mothur_unique_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_tree_shared, mothur_count_seqs, mothur_cluster, mothur_summary_seqs, mothur_remove_groups	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.fr	5649	9534	4.583333
Microbiome	16S Microbial Analysis with mothur (extended)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding	Phylogenetic tree reconstruction, Sequencing quality control, DNA barcoding, Sequence read processing, Sequence clustering, Phylogenetic tree analysis, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree generation, Visualisation	2017-02-12	2025-12-18	5	True	False	False	True	mothur_dist_shared, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_make_contigs, mothur_make_shared, XY_Plot_1, mothur_heatmap_sim, mothur_filter_seqs, mothur_summary_single, mothur_venn, newick_display, mothur_count_groups, taxonomy_krona_chart, mothur_align_seqs, mothur_dist_seqs, mothur_rarefaction_single, mothur_pre_cluster, mothur_get_groups, mothur_sub_sample, mothur_seq_error, mothur_remove_seqs, mothur_classify_seqs, mothur_make_biom, mothur_unique_seqs, mothur_remove_lineage, mothur_classify_otu, mothur_tree_shared, mothur_count_seqs, mothur_cluster, mothur_taxonomy_to_krona, mothur_summary_seqs, mothur_remove_groups	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	12390	18175	2.750000
Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Sequence composition calculation, Sequencing quality control, Global alignment, Local alignment, Statistical calculation, Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction, Validation, Sequence analysis, Taxonomic classification, Phylogenetic tree generation, Sequence alignment, Sequence alignment analysis, Genome visualisation, Sequence contamination filtering	2020-07-25	2025-11-18	31	True	False	True	True	bcftools_consensus, EMBOSS:%20seqret84, tb_variant_filter, upload1, __FLATTEN__, snippy, fastp, tp_awk_tool, tbvcfreport, jbrowse, EMBOSS: seqret84, fastqc, samtools_stats, qualimap_bamqc, mosdepth, jvarkit_wgscoverageplotter, multiqc, kraken2, tp_sed_tool, tb_profiler_profile			7631	11755	3.000000
Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Query and retrieval, Statistical inference, Principal component visualisation, Heat map generation, Filtering, Differential protein expression analysis, Indexing, Quantification, Functional clustering, Visualisation	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_sample, metaquantome_db, metaquantome_filter, metaquantome_stat, metaquantome_viz, metaquantome_expand	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	449	587	2.250000
Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation	2017-06-28	2024-06-14	41	True	False	True	True	peptide_shaker, unipept, query_tabular, sqlite_to_tabular, search_gui	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	2930	4652	2.716667
Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Query and retrieval, Statistical inference, Principal component visualisation, Heat map generation, Filtering, Differential protein expression analysis, Indexing, Quantification, Functional clustering, Visualisation	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_sample, metaquantome_db, metaquantome_filter, metaquantome_stat, metaquantome_viz, metaquantome_expand	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	422	593	4.133333
Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Filtering, Label-free quantification, Formatting, Prediction and recognition, Visualisation	2020-10-16	2024-03-14	20	True	False	False	True	tp_replace_in_column, msconvert, Remove beginning1, peptide_shaker, Cut1, flashlfq, unipept, query_tabular, search_gui, tp_replace_in_line, regex1, Grep1, Filter1	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	893	1507	3.733333
Sequence analysis	Quality and contamination control in bacterial isolate using Illumina MiSeq Data	https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Sequencing quality control, Statistical calculation, Expression analysis, Taxonomic classification, Sequence contamination filtering, Cross-assembly, Visualisation, Read mapping	2024-07-15	2025-12-18	5	True	False	True	True	recentrifuge, falco, upload1, kraken2, est_abundance, fastp	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		1731	2343	2.750000
Variant Analysis	Calling variants in non-diploid systems	https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Sequence composition calculation, Sequencing quality control, Genome indexing, Statistical calculation, Variant calling, Generation, Data handling, Formatting, Sequence alignment, Sequence alignment analysis, Read mapping	2017-02-16	2024-03-15	23	True	False	False	True	picard_MergeSamFiles, freebayes, Cut1, bamleftalign, picard_MarkDuplicates, fastqc, vcf2tsv, bamFilter, bwa_mem, vcffilter2	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	8914	15830	2.083333