Expand	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	Feedback number	Feedback mean note	Visitors	Page views	Visit duration	Video views
	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	Statistical calculation, Genome assembly, Sequence alignment, Sequence contamination filtering, Sequence assembly validation, Cross-assembly, Sequence composition calculation, Scatter plot plotting, Filtering, Mapping assembly, Visualisation, De-novo assembly, Box-Whisker plot plotting, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequencing error detection	2021-03-24	2026-01-05	16	True	False	False	True	fastqc, __FLATTEN__, bwa_mem2, fastp, quast, bandage_image, __EXTRACT_DATASET__, filtlong, nanoplot, polypolish, CONVERTER_bz2_to_uncompressed, flye, porechop, upload1	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr	0		10807	16115	3.366667	0
	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	Visualisation, Genome assembly, Sequence contamination filtering, Sequence assembly visualisation, Read mapping, Sequencing quality control, Sequence assembly validation	2021-03-24	2026-01-05	18	True	False	True	True	shovill, fastp, quast, falco, upload1, bandage_image, bandage_info	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		0		10653	16340	3.566667	0
	Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Sequence alignment analysis, Statistical calculation, Genome assembly, Sequence file editing, Local alignment, Sequence contamination filtering, Variant calling, Sequence trimming, Sequence composition calculation, Formatting, Data handling, Primer removal, Visualisation, Read pre-processing, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequence assembly validation	2026-02-10	2026-02-10	0	True	False	True	True	bowtie2, fastqc, bg_uniq, quast, coverm_contig, metaspades, collection_column_join, filter_tabular, bamtools, cutadapt, megahit, ngsutils_bam_filter, bandage_image, megahit_contig2fastg, tp_cat, seqtk_subseq, random_lines1, bandage_info		UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)	0		2	3	0.000000	0
	Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Aggregation, Statistical calculation, Genome assembly, Gene prediction, Visualisation, Validation, Coding region prediction, Genome annotation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation	2017-10-11	2026-01-23	25	True	True	False	True	fastqc, quast, multiqc, prokka, unicycler	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		3456485	8425505	4.233333	0
	Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome visualisation, Sequence alignment, Mapping, Sequence visualisation, Read mapping	2018-06-14	2024-06-24	29	True	False	False	True	collapse_dataset, jbrowse, circos_aln_to_links, tp_grep_tool, join1, tp_cat, tp_sed_tool, addValue, Filter1, fasta_compute_length, bedtools_sortbed, fasta_filter_by_length, bedtools_intersectbed, circos_interval_to_tiles, tp_sort_header_tool, mergeCols1, lastz_wrapper_2, random_lines1, upload1, tp_replace_in_column, Cut1, datamash_ops, cat1, tp_replace_in_line, bedtools_complementbed, Grep1, circos			0		6820	13073	2.916667	0
	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	Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification	2024-03-04	2025-12-18	5	True	False	False	True	est_abundance, kraken2, recentrifuge, upload1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main)	0		947	1266	3.183333	0
	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	Phylogenetic tree generation, Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction	2022-03-16	2025-05-26	13	True	False	False	True	collapse_dataset, bcftools_consensus, clustering_from_distmat, trimmomatic, tp_grep_tool, addName, tp_cat, tp_sed_tool, tb_profiler_profile, snp_sites, tb_variant_filter, upload1, __MERGE_COLLECTION__, tp_replace_in_line, tp_easyjoin_tool, snp_dists, snippy, samtools_view, Grep1	UseGalaxy.eu		0		3112	4436	2.600000	0
	Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Sequence analysis, Phylogenetic tree analysis	2022-03-16	2025-06-04	12	True	False	False	True	interactive_tool_rstudio, upload1, raxml	UseGalaxy.eu		0		2341	3360	2.450000	0
	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 (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	2025-03-14	2025-03-14	1	True	False	False	False	fasttree, upload1	Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	GalaxyTrakr	0		133	155	1.900000	0
	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	Coding region prediction, Genome annotation, Genome visualisation, Gene prediction	2018-03-06	2026-01-23	27	True	True	True	True	jbrowse, prokka	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		3462475	8435376	4.100000	0
	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, Genome visualisation, Antimicrobial resistance prediction, Read mapping	2024-01-23	2025-12-18	10	True	False	True	True	bowtie2, tbl2gff3, jbrowse, staramr_search, upload1, Grep1, bakta	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main)	0		3781	5160	2.866667	0
	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	iframe, list_organism, jbrowse, create_account, create_or_update	UseGalaxy.be	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		3218354	7626702	4.933333	0
	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	Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome assembly, Nucleic acid feature detection, Scaffolding, Protein feature detection, Genome annotation, Structural variation detection	2024-02-01	2024-10-15	6	True	False	True	True	tbl2gff3, tp_replace_in_column, integron_finder, jbrowse, isescan, upload1, plasmidfinder, tp_tail_tool, Grouping1, bakta	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		7182	9815	2.650000	0
	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	Data handling, Data retrieval, Sequence database search	2025-03-14	2025-03-14	1	True	False	False	False	bg_uniq, datasets_download_genome, Cut1, sort1, cat1, Remove beginning1, upload1	UseGalaxy.fr	UseGalaxy.cz	0		94	112	2.333333	0
	Genome Annotation	Bacterial genome quality control	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html	Genomics, Microbiology	Genome comparison, Statistical calculation, Validation, Sequence composition calculation, Sequencing quality control, Sequence assembly 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	0		117	129	1.616667	0
	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	Sequence alignment analysis, Transcriptome assembly, Database search, Phylogenetic tree generation, Coding region prediction, Multiple sequence alignment, De-novo assembly	2022-09-08	2025-06-03	10	True	False	False	True	tp_split_on_column, rbc_mafft, Cut1, orfipy, bg_diamond_view, collapse_dataset, cat1, Add_a_column1, bg_diamond, gops_intersect_1, tab2fasta, Filter1, regexColumn1, bg_diamond_makedb, join1, rapidnj	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		1948	2707	2.983333	0
	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	Cut1, Add_a_column1, bowtie_wrapper, transit_gumbel, __EXTRACT_DATASET__, gff_to_prot, tp_sort_header_tool, bg_find_subsequences, Filter1, cutadapt, tp_easyjoin_tool, deeptools_bam_coverage	UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		3451941	8418427	3.900000	0
	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	Phylogenetic tree generation, Variant calling, Genome visualisation, Phylogenetic tree visualisation	2018-02-26	2026-01-23	25	True	False	False	True	snippy, jbrowse	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		15579	24719	2.050000	0
	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	Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding, Sequencing quality control	2017-06-22	2024-08-09	4	True	False	False	True	metaphlan2krona, mothur_filter_seqs, mothur_unique_seqs, humann2_regroup_table, mothur_classify_seqs, mothur_merge_files, mothur_screen_seqs, metaphlan2, mothur_align_seqs, mothur_count_seqs, mothur_cluster_split, mothur_pre_cluster, krona-text, taxonomy_krona_chart, humann2_renorm_table, mothur_make_biom, mothur_summary_seqs, humann2, mothur_make_shared, mothur_make_group, mothur_classify_otu	UseGalaxy.be	UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		9597	13111	2.650000	0
	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	Scatter plot plotting, Aggregation, Genome assembly, Sequence analysis, Mapping assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Pairwise sequence alignment, De-novo assembly, Antimicrobial resistance prediction	2019-06-25	2024-06-14	4	True	False	True	True	PlasFlow, unicycler, bandage_image, miniasm, minimap2, gfa_to_fa, staramr_search, racon, nanoplot	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		3658	5104	2.883333	0
	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	Sequence alignment analysis, Phylogenetic tree reconstruction, Statistical calculation, Genome assembly, Mapping, Antimicrobial resistance prediction, Sequence contamination filtering, Variant calling, Sequence assembly, Cross-assembly, Sequence composition calculation, Phylogenetic tree generation, Aggregation, Scatter plot plotting, Multilocus sequence typing, Sequencing quality control, Data handling, Multiple sequence alignment, Taxonomic classification, Phylogenetic tree analysis, Visualisation, Mapping assembly, De-novo assembly, Box-Whisker plot plotting, Validation, Phylogenetic tree generation (from molecular sequences), Sequence assembly visualisation, Pairwise sequence alignment, Base-calling, Phylogenetic tree generation (maximum likelihood and Bayesian methods)	2023-01-26	2025-11-18	12	True	False	True	True	split_file_to_collection, bamtools_split_mapped, clair3, tp_find_and_replace, compose_text_param, table_compute, collapse_dataset, tp_head_tool, tab2fasta, bcftools_consensus, snpSift_extractFields, snpSift_filter, Grep1, Count1, medaka_consensus_pipeline, tp_cut_tool, samtools_fastx, fastqc, krakentools_kreport2krona, fastp, tp_sorted_uniq, multiqc, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, minimap2, __FILTER_FAILED_DATASETS__, __BUILD_LIST__, fasttree, Paste1, tp_split_on_column, __FILTER_EMPTY_DATASETS__, tp_multijoin_tool, bcftools_norm, ggplot2_heatmap, clustalw, collection_element_identifiers, krakentools_extract_kraken_reads, collection_column_join, param_value_from_file, mlst, samtools_depth, samtools_coverage, kraken2, regex1, nanoplot, CONVERTER_gz_to_uncompressed, taxonomy_krona_chart, fasta2tab, porechop, tp_replace_in_column, Cut1, bedtools_getfastabed, barchart_gnuplot, Add_a_column1, abricate, regexColumn1, add_line_to_file, bandage_image, newick_display, flye, Grouping1	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.org.au	0		5208	7681	3.200000	0
	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	Visualisation, Statistical calculation, Genome annotation, Taxonomic classification, Aggregation	2023-05-03	2025-12-18	7	True	False	True	True	est_abundance, krakentools_kreport2krona, interactive_tool_pavian, __UNZIP_COLLECTION__, interactive_tool_phinch, metaphlan, kraken2, kraken_biom, taxonomy_krona_chart	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		0		13113	17458	1.983333	0
	Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Sequence alignment analysis, Statistical calculation, Genome assembly, Sequence file editing, Local alignment, Sequence contamination filtering, Variant calling, Sequence trimming, Sequence composition calculation, Formatting, Data handling, Primer removal, Visualisation, Read pre-processing, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequence assembly validation	2022-12-05	2025-12-08	8	True	False	True	True	bowtie2, fastqc, bg_uniq, quast, coverm_contig, metaspades, collection_column_join, filter_tabular, bamtools, cutadapt, megahit, ngsutils_bam_filter, bandage_image, megahit_contig2fastg, tp_cat, seqtk_subseq, random_lines1, bandage_info		UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)	0		4744	6551	2.883333	0
	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	Analysis, Visualisation, DNA barcoding, Variant calling, Deposition	2024-06-05	2025-07-03	11	True	False	True	True	interactive_tool_phyloseq, dada2_filterAndTrim, dada2_mergePairs, tp_head_tool, dada2_assignTaxonomyAddspecies, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_dada, dada2_removeBimeraDenovo, __SORTLIST__, dada2_plotQualityProfile, collection_element_identifiers, dada2_learnErrors, dada2_seqCounts, tp_replace_in_column, __UNZIP_COLLECTION__, cat1, Add_a_column1, tp_replace_in_line, Grouping1	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		0		7686	10865	2.350000	0
	Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Genome comparison, Statistical calculation, Sequencing quality control, Sequence clustering, Validation, Read binning, Genome annotation, Sequence assembly, Sequence composition calculation, Read mapping, Sequence assembly validation	2023-12-05	2025-12-02	7	True	False	True	True	bowtie2, maxbin2, samtools_sort, concoct, das_tool, metabat2_jgi_summarize_bam_contig_depths, concoct_cut_up_fasta, concoct_coverage_table, drep_dereplicate, concoct_merge_cut_up_clustering, __BUILD_LIST__, checkm_lineage_wf, metabat2, semibin, concoct_extract_fasta_bins, Fasta_to_Contig2Bin, binette	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main), UseGalaxy.org.au	0		6118	7485	1.433333	0
	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	Visualisation, Statistical calculation, Validation, Sequence contamination filtering, Taxonomic classification, Sequence composition calculation, Sequencing quality control	2020-11-24	2024-07-31	5	True	False	False	True	fastqc, fastp, multiqc, Remove beginning1, tp_replace_in_line, kraken2, datamash_reverse, taxonomy_krona_chart, porechop	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	0		9037	12557	2.650000	0
	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	Visualisation, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Sequence composition calculation, Sequencing quality control, Aggregation	2022-09-29	2024-11-29	5	True	False	True	True	fastqc, krakentools_kreport2krona, fastp, Filter1, kraken2, taxonomy_krona_chart, porechop	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		3083	4474	2.800000	0
	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 similarity search, Sequence alignment analysis, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence trimming, Sequence composition calculation, Phylogenetic tree editing, Conversion, Sequence comparison, Primer removal, Taxonomic classification, Read pre-processing, Visualisation, Validation, Phylogenetic inference, Sequencing quality control	2020-02-13	2025-06-16	6	True	False	True	True	humann_rename_table, graphlan_annotate, tp_find_and_replace, fastq_paired_end_interlacer, metaphlan, graphlan, fastqc, humann_split_stratified_table, multiqc, bg_sortmerna, humann_regroup_table, cutadapt, export2graphlan, combine_metaphlan2_humann2, humann_renorm_table, tp_sort_header_tool, taxonomy_krona_chart, Cut1, humann, humann_unpack_pathways, Grep1	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		859	1115	2.366667	0
	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	Sequence similarity search, Sequence alignment analysis, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence trimming, Sequence composition calculation, Phylogenetic tree editing, Conversion, Sequence comparison, Primer removal, Taxonomic classification, Read pre-processing, Visualisation, Validation, Phylogenetic inference, Sequencing quality control, Aggregation	2019-11-21	2025-06-16	6	True	True	True	True	humann_rename_table, graphlan_annotate, tp_find_and_replace, fastq_paired_end_interlacer, metaphlan, graphlan, fastqc, humann_split_stratified_table, multiqc, bg_sortmerna, humann_regroup_table, cutadapt, export2graphlan, humann_renorm_table, tp_sort_header_tool, taxonomy_krona_chart, Cut1, humann, humann_unpack_pathways, Grep1, combine_metaphlan_humann, Grouping1	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.eu	0		3450732	8412774	4.066667	0
	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	0		444	716	3.083333	0
	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	Genome comparison, Statistical calculation, Data handling, Validation, Genome annotation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation	2025-12-18	2025-12-18	1	True	False	False	False	tp_replace_in_column, Cut1, collapse_dataset, multiqc, cat1, Remove beginning1, fasterq_dump, collection_column_join, drep_dereplicate, __EXTRACT_DATASET__, Summary_Statistics1, tp_sort_header_tool, checkm_lineage_wf, bakta, join1, Grouping1	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		221	262	1.433333	0
	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	0		670	1007	2.400000	0
	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, Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Visualisation, DNA barcoding, Phylogenetic tree generation, Sequencing quality control	2019-05-13	2025-12-18	6	True	False	True	True	mothur_summary_single, mothur_filter_seqs, collapse_dataset, mothur_dist_seqs, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_classify_seqs, mothur_dist_shared, mothur_tree_shared, mothur_screen_seqs, mothur_chimera_vsearch, mothur_remove_lineage, mothur_count_groups, XY_Plot_1, mothur_count_seqs, mothur_venn, mothur_cluster_split, mothur_pre_cluster, mothur_rarefaction_single, mothur_heatmap_sim, mothur_remove_groups, mothur_summary_seqs, mothur_make_shared, mothur_sub_sample, newick_display, mothur_classify_otu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.fr	0		6078	10180	4.466667	0
	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, Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Visualisation, DNA barcoding, Phylogenetic tree generation, Sequencing quality control	2017-02-12	2025-12-18	5	True	False	False	True	mothur_summary_single, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_classify_seqs, mothur_seq_error, mothur_dist_shared, mothur_tree_shared, mothur_make_contigs, mothur_screen_seqs, mothur_get_groups, mothur_chimera_vsearch, mothur_align_seqs, mothur_remove_lineage, mothur_count_groups, XY_Plot_1, mothur_count_seqs, mothur_venn, mothur_cluster_split, mothur_pre_cluster, taxonomy_krona_chart, mothur_rarefaction_single, mothur_make_biom, mothur_heatmap_sim, mothur_remove_groups, mothur_summary_seqs, mothur_make_shared, mothur_sub_sample, mothur_taxonomy_to_krona, newick_display, mothur_classify_otu	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		12935	18943	2.733333	0
	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 alignment analysis, Genome visualisation, Statistical calculation, Global alignment, Sequence analysis, Taxonomic classification, Local alignment, Phylogenetic tree visualisation, Validation, Sequence alignment, Sequence contamination filtering, Phylogenetic tree generation, Variant calling, Sequence composition calculation, Sequencing quality control, Antimicrobial resistance prediction	2020-07-25	2026-01-06	32	True	False	True	True	qualimap_bamqc, jbrowse, samtools_stats, bcftools_consensus, fastqc, fastp, EMBOSS: seqret84, multiqc, tp_sed_tool, tp_awk_tool, tb_profiler_profile, EMBOSS:%20seqret84, jvarkit_wgscoverageplotter, kraken2, tb_variant_filter, upload1, tbvcfreport, __FLATTEN__, mosdepth, snippy			0		7924	12096	2.900000	0
	Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Statistical inference, Functional clustering, Query and retrieval, Principal component visualisation, Heat map generation, Filtering, Visualisation, Indexing, Quantification, Differential protein expression analysis	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		458	598	2.216667	0
	Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Visualisation, Prediction and recognition	2017-06-28	2024-06-14	41	True	False	True	True	search_gui, unipept, sqlite_to_tabular, query_tabular, peptide_shaker	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2995	4731	2.666667	0
	Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Statistical inference, Functional clustering, Query and retrieval, Principal component visualisation, Heat map generation, Filtering, Visualisation, Indexing, Quantification, Differential protein expression analysis	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		437	608	4.033333	0
	Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Formatting, Visualisation, Filtering, Label-free quantification, Prediction and recognition	2020-10-16	2024-03-14	20	True	False	False	True	tp_replace_in_column, Cut1, search_gui, Remove beginning1, msconvert, unipept, tp_replace_in_line, Filter1, flashlfq, regex1, query_tabular, Grep1, peptide_shaker	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		909	1526	3.750000	0
	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	Statistical calculation, Expression analysis, Taxonomic classification, Visualisation, Sequence contamination filtering, Read mapping, Cross-assembly, Sequencing quality control	2024-07-15	2025-12-18	5	True	False	True	True	est_abundance, recentrifuge, fastp, falco, kraken2, upload1	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		0		1826	2467	2.700000	0
	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	Formatting, Sequence alignment analysis, Statistical calculation, Data handling, Genome indexing, Generation, Sequence alignment, Read mapping, Variant calling, Sequence composition calculation, Sequencing quality control	2017-02-16	2024-03-15	23	True	False	False	True	fastqc, freebayes, Cut1, picard_MarkDuplicates, bwa_mem, vcffilter2, picard_MergeSamFiles, bamFilter, vcf2tsv, bamleftalign	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		9453	16432	2.000000	0