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	Sequence contamination filtering, Filtering, Mapping assembly, Visualisation, Scatter plot plotting, Genome assembly, Read mapping, Cross-assembly, Sequence composition calculation, De-novo assembly, Sequencing quality control, Sequence assembly validation, Sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Statistical calculation, Sequencing error detection	2021-03-24	2024-11-29	15	True	False	False	True	upload1, flye, filtlong, quast, nanoplot, bandage_image, polypolish, porechop, fastqc, CONVERTER_bz2_to_uncompressed, fastp, bwa_mem2	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr	0		10547	15790	3.400000	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	Sequence contamination filtering, Read mapping, Visualisation, Genome assembly, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Sequence assembly visualisation, Statistical calculation	2021-03-24	2025-11-18	17	True	False	True	True	upload1, quast, bandage_image, fastqc, fastp, bandage_info, falco, shovill	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		0		10291	15797	3.550000	0
	Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Sequence alignment analysis, Read mapping, Genome assembly, Sequence trimming, Sequence file editing, Sequence assembly validation, Sequence assembly visualisation, Variant calling, Statistical calculation, Sequence contamination filtering, Visualisation, Read pre-processing, Sequence composition calculation, Formatting, Sequencing quality control, Primer removal, Local alignment, Data handling	2025-12-07	2025-12-07	0	True	False	True	True	coverm_contig, random_lines1, bamtools, tp_cat, cutadapt, ngsutils_bam_filter, quast, megahit, bg_uniq, filter_tabular, bandage_image, collection_column_join, megahit_contig2fastg, metaspades, bowtie2, fastqc, bandage_info, seqtk_subseq		UseGalaxy.cz, UseGalaxy.eu	0		1	1	0.000000	0
	Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Visualisation, Genome assembly, Gene prediction, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Genome annotation, Aggregation, Coding region prediction, Statistical calculation, Validation	2017-10-11	2025-05-15	24	True	True	False	True	quast, multiqc, fastqc, prokka, unicycler	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		3097980	7936496	4.400000	0
	Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Read mapping, Sequence alignment, Mapping, Genome visualisation, Sequence visualisation	2018-06-14	2024-06-24	29	True	False	False	True	bedtools_complementbed, jbrowse, circos_aln_to_links, tp_sed_tool, Grep1, upload1, circos_interval_to_tiles, lastz_wrapper_2, collapse_dataset, cat1, bedtools_intersectbed, Filter1, mergeCols1, tp_sort_header_tool, tp_cat, addValue, random_lines1, tp_grep_tool, bedtools_sortbed, join1, fasta_filter_by_length, Cut1, circos, tp_replace_in_line, fasta_compute_length, tp_replace_in_column, datamash_ops			0		6769	13021	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	Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation	2024-03-04	2024-06-27	4	True	False	False	True	est_abundance, kraken2, recentrifuge, upload1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		886	1180	3.283333	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	Variant calling, Phylogenetic tree generation, Antimicrobial resistance prediction, Phylogenetic tree visualisation	2022-03-16	2025-05-26	13	True	False	False	True	snippy, tb_profiler_profile, tp_sed_tool, clustering_from_distmat, Grep1, upload1, __MERGE_COLLECTION__, tb_variant_filter, collapse_dataset, bcftools_consensus, snp_dists, trimmomatic, tp_cat, tp_easyjoin_tool, addName, snp_sites, tp_grep_tool, samtools_view, tp_replace_in_line	UseGalaxy.eu		0		2956	4250	2.666667	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	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu		0		2271	3278	2.483333	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 (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	0		102	124	2.516667	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	Genome annotation, Gene prediction, Genome visualisation, Coding region prediction	2018-03-06	2025-03-19	26	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		3103802	7946069	4.250000	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	Read mapping, Antimicrobial resistance prediction, Genome visualisation, Genome annotation	2024-01-23	2025-06-10	9	True	False	True	True	upload1, staramr_search, jbrowse, bowtie2, tbl2gff3, bakta, Grep1	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		3531	4879	3.016667	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	jbrowse, iframe, create_or_update, list_organism, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		2859955	7137749	5.100000	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	Nucleic acid feature detection, Genome assembly, Protein feature detection, Genome visualisation, Structural variation detection, Multilocus sequence typing, Genome annotation, Scaffolding, Sequence motif recognition	2024-02-01	2024-10-15	6	True	False	True	True	upload1, tp_tail_tool, jbrowse, Grouping1, isescan, integron_finder, tbl2gff3, bakta, tp_replace_in_column, plasmidfinder	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		6578	8946	2.616667	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	Sequence database search, Data retrieval, Data handling	2025-03-14	2025-03-14	1	True	False	False	False	upload1, sort1, bg_uniq, Cut1, Remove beginning1, datasets_download_genome, cat1	UseGalaxy.fr	UseGalaxy.cz	0		84	102	3.033333	0
	Genome Annotation	Bacterial genome quality control	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html	Genomics, Microbiology	Sequencing quality control, Sequence assembly validation, Validation, Genome comparison, Sequence composition calculation, Statistical calculation	2025-03-14	2025-03-14	1	True	False	False	False	upload1, checkm2, drep_dereplicate	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz	0		92	102	2.183333	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	Database search, Sequence alignment analysis, Coding region prediction, Transcriptome assembly, Multiple sequence alignment, De-novo assembly, Phylogenetic tree generation	2022-09-08	2025-06-03	10	True	False	False	True	tab2fasta, tp_split_on_column, rbc_mafft, join1, collapse_dataset, rapidnj, Cut1, Add_a_column1, bg_diamond, cat1, bg_diamond_makedb, Filter1, gops_intersect_1, regexColumn1, bg_diamond_view, orfipy	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		1869	2620	3.033333	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	Primer removal, Read pre-processing, Transposon prediction, Sequence trimming	2019-07-02	2024-03-18	12	True	True	False	True	cutadapt, transit_gumbel, bowtie_wrapper, __EXTRACT_DATASET__, deeptools_bam_coverage, Cut1, bg_find_subsequences, Add_a_column1, gff_to_prot, tp_easyjoin_tool, Filter1, tp_sort_header_tool	UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		3093269	7929187	4.066667	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 visualisation, Variant calling, Genome visualisation, Phylogenetic tree generation	2018-02-26	2025-03-19	24	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		15187	24237	2.033333	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	Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering	2017-06-22	2024-08-09	4	True	False	False	True	mothur_align_seqs, mothur_merge_files, krona-text, mothur_classify_otu, mothur_classify_seqs, taxonomy_krona_chart, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, metaphlan2, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_screen_seqs, mothur_make_biom, metaphlan2krona, mothur_make_group, humann2_renorm_table, mothur_cluster_split, humann2_regroup_table, humann2		UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		8775	11972	2.683333	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	Antimicrobial resistance prediction, Scatter plot plotting, Mapping assembly, Genome assembly, Sequence analysis, De-novo assembly, Aggregation, Box-Whisker plot plotting, Sequence assembly visualisation, Pairwise sequence alignment	2019-06-25	2024-06-14	4	True	False	True	True	minimap2, unicycler, staramr_search, PlasFlow, nanoplot, bandage_image, miniasm, gfa_to_fa, racon	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		3257	4555	3.000000	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	Base-calling, Sequence alignment analysis, Mapping assembly, Taxonomic classification, Genome assembly, Cross-assembly, De-novo assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multilocus sequence typing, Aggregation, Mapping, Sequence assembly, Box-Whisker plot plotting, Variant calling, Sequence assembly visualisation, Pairwise sequence alignment, Phylogenetic tree generation, Sequence contamination filtering, Phylogenetic tree reconstruction, Antimicrobial resistance prediction, Visualisation, Scatter plot plotting, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Multiple sequence alignment, Sequence composition calculation, Sequencing quality control, Statistical calculation, Data handling, Validation	2023-01-26	2025-11-18	12	True	False	True	True	split_file_to_collection, flye, bcftools_norm, bedtools_getfastabed, fasta2tab, clair3, collection_column_join, fastqc, samtools_depth, Grep1, newick_display, fasttree, fasta_merge_files_and_filter_unique_sequences, abricate, samtools_coverage, tp_multijoin_tool, collapse_dataset, taxonomy_krona_chart, Remove beginning1, Grouping1, bcftools_consensus, porechop, ggplot2_heatmap, tp_cut_tool, samtools_fastx, __FILTER_FAILED_DATASETS__, compose_text_param, regexColumn1, CONVERTER_gz_to_uncompressed, minimap2, barchart_gnuplot, tp_split_on_column, Paste1, kraken2, medaka_consensus_pipeline, tp_find_and_replace, collection_element_identifiers, tp_sorted_uniq, multiqc, krakentools_extract_kraken_reads, snpSift_filter, clustalw, __BUILD_LIST__, tab2fasta, __FILTER_EMPTY_DATASETS__, Count1, tp_head_tool, fastp, krakentools_kreport2krona, mlst, Cut1, Add_a_column1, regex1, bamtools_split_mapped, bandage_image, nanoplot, table_compute, snpSift_extractFields, param_value_from_file, tp_replace_in_column, add_line_to_file	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.org.au	0		4828	7227	3.366667	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, Genome annotation, Taxonomic classification, Aggregation, Statistical calculation	2023-05-03	2025-04-24	6	True	False	True	True	interactive_tool_phinch, kraken2, krakentools_kreport2krona, taxonomy_krona_chart, est_abundance, __UNZIP_COLLECTION__, metaphlan, kraken_biom, interactive_tool_pavian	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		0		12235	16305	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, Read mapping, Genome assembly, Sequence trimming, Sequence file editing, Sequence assembly validation, Sequence assembly visualisation, Variant calling, Statistical calculation, Sequence contamination filtering, Visualisation, Read pre-processing, Sequence composition calculation, Formatting, Sequencing quality control, Primer removal, Local alignment, Data handling	2022-12-05	2025-06-16	6	True	False	True	True	coverm_contig, random_lines1, bamtools, tp_cat, cutadapt, ngsutils_bam_filter, quast, megahit, bg_uniq, filter_tabular, bandage_image, collection_column_join, megahit_contig2fastg, metaspades, bowtie2, fastqc, bandage_info, seqtk_subseq		UseGalaxy.cz, UseGalaxy.eu	0		4399	6128	3.000000	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	Visualisation, Analysis, DNA barcoding, Deposition, Variant calling	2024-06-05	2025-07-03	11	True	False	True	True	phyloseq_from_dada2, dada2_learnErrors, dada2_dada, dada2_makeSequenceTable, dada2_removeBimeraDenovo, dada2_seqCounts, Grouping1, __SORTLIST__, cat1, dada2_mergePairs, dada2_filterAndTrim, dada2_plotQualityProfile, dada2_assignTaxonomyAddspecies, collection_element_identifiers, interactive_tool_phyloseq, tp_head_tool, Add_a_column1, __UNZIP_COLLECTION__, tp_replace_in_line, tp_replace_in_column	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au		0		7044	9924	2.333333	0
	Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Read mapping, Genome comparison, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Genome annotation, Read binning, Sequence assembly, Sequence clustering, Statistical calculation, Validation	2023-12-05	2025-12-02	7	True	False	True	True	concoct_coverage_table, checkm_lineage_wf, samtools_sort, concoct_extract_fasta_bins, drep_dereplicate, binette, concoct, maxbin2, concoct_merge_cut_up_clustering, bowtie2, Fasta_to_Contig2Bin, semibin, das_tool, concoct_cut_up_fasta, metabat2_jgi_summarize_bam_contig_depths, __BUILD_LIST__, metabat2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main), UseGalaxy.org.au	0		5593	6834	1.466667	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	Statistical calculation, Sequence contamination filtering, Sequencing quality control, Visualisation, Taxonomic classification, Sequence composition calculation, Validation	2020-11-24	2024-07-31	5	True	False	False	True	kraken2, taxonomy_krona_chart, Remove beginning1, multiqc, datamash_reverse, porechop, fastqc, tp_replace_in_line, fastp	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	0		8182	11295	2.616667	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	Sequence contamination filtering, Sequencing quality control, Visualisation, Taxonomic classification, Aggregation, Sequence composition calculation, Statistical calculation	2022-09-29	2024-11-29	5	True	False	True	True	kraken2, krakentools_kreport2krona, taxonomy_krona_chart, porechop, fastqc, Filter1, fastp	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		2666	3886	2.866667	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 alignment analysis, Phylogenetic inference, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree editing, Sequence trimming, Sequence similarity search, Sequence comparison, Visualisation, Read pre-processing, Sequence composition calculation, Species frequency estimation, Sequencing quality control, Primer removal, Conversion, Statistical calculation, Validation, Phylogenetic tree visualisation	2020-02-13	2025-06-16	6	True	False	True	True	humann_renorm_table, export2graphlan, metaphlan, fastqc, humann_split_stratified_table, fastq_paired_end_interlacer, Grep1, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_sort_header_tool, cutadapt, tp_find_and_replace, multiqc, graphlan, graphlan_annotate, bg_sortmerna, Cut1, humann_regroup_table, humann, humann_unpack_pathways, humann_rename_table	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		785	1024	2.433333	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 alignment analysis, Phylogenetic inference, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree editing, Sequence trimming, Sequence similarity search, Aggregation, Sequence comparison, Visualisation, Read pre-processing, Sequence composition calculation, Species frequency estimation, Sequencing quality control, Primer removal, Conversion, Statistical calculation, Validation, Phylogenetic tree visualisation	2019-11-21	2025-06-16	6	True	True	True	True	humann_renorm_table, export2graphlan, metaphlan, fastqc, humann_split_stratified_table, fastq_paired_end_interlacer, Grep1, taxonomy_krona_chart, Grouping1, tp_sort_header_tool, combine_metaphlan_humann, cutadapt, tp_find_and_replace, multiqc, graphlan, graphlan_annotate, bg_sortmerna, Cut1, humann_regroup_table, humann, humann_unpack_pathways, humann_rename_table	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.eu	0		3091750	7923137	4.300000	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		412	664	3.150000	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		583	896	2.733333	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, Visualisation, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree generation	2019-05-13	2024-06-14	5	True	False	True	True	mothur_count_groups, mothur_summary_single, XY_Plot_1, mothur_remove_lineage, newick_display, mothur_classify_otu, mothur_classify_seqs, collapse_dataset, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, mothur_remove_seqs, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_remove_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_cluster, mothur_screen_seqs, mothur_dist_seqs, mothur_dist_shared, mothur_heatmap_sim, mothur_tree_shared, mothur_rarefaction_single, mothur_venn, mothur_cluster_split	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.fr	0		5460	9209	4.583333	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, Visualisation, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree generation	2017-02-12	2024-03-14	4	True	False	False	True	mothur_count_groups, mothur_summary_single, XY_Plot_1, mothur_make_contigs, mothur_align_seqs, mothur_remove_lineage, mothur_seq_error, newick_display, mothur_classify_otu, mothur_classify_seqs, taxonomy_krona_chart, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, mothur_remove_seqs, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_remove_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_cluster, mothur_screen_seqs, mothur_make_biom, mothur_dist_seqs, mothur_taxonomy_to_krona, mothur_dist_shared, mothur_heatmap_sim, mothur_tree_shared, mothur_rarefaction_single, mothur_venn, mothur_cluster_split, mothur_get_groups	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		12182	17924	2.783333	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, Sequence contamination filtering, Antimicrobial resistance prediction, Taxonomic classification, Sequence analysis, Genome visualisation, Sequence composition calculation, Sequencing quality control, Sequence alignment, Phylogenetic tree generation, Validation, Variant calling, Local alignment, Global alignment, Statistical calculation, Phylogenetic tree visualisation	2020-07-25	2025-11-18	31	True	False	True	True	EMBOSS: seqret84, samtools_stats, snippy, tb_profiler_profile, jbrowse, tp_sed_tool, EMBOSS:%20seqret84, fastqc, mosdepth, upload1, tb_variant_filter, qualimap_bamqc, bcftools_consensus, tp_awk_tool, kraken2, multiqc, jvarkit_wgscoverageplotter, __FLATTEN__, tbvcfreport, fastp			0		7526	11623	3.000000	0
	Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Quantification, Heat map generation, Indexing, Filtering, Visualisation, Differential protein expression analysis, Principal component visualisation, Statistical inference, Query and retrieval, Functional clustering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db, metaquantome_stat	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		448	586	2.250000	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, peptide_shaker, query_tabular	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2916	4634	2.700000	0
	Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Quantification, Heat map generation, Indexing, Filtering, Visualisation, Differential protein expression analysis, Principal component visualisation, Statistical inference, Query and retrieval, Functional clustering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db, metaquantome_stat	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		421	592	4.166667	0
	Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Filtering, Visualisation, Label-free quantification, Prediction and recognition, Formatting	2020-10-16	2024-03-14	20	True	False	False	True	search_gui, unipept, Cut1, Remove beginning1, msconvert, regex1, peptide_shaker, tp_replace_in_line, Filter1, flashlfq, tp_replace_in_column, Grep1, query_tabular	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		892	1506	3.733333	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	Sequence contamination filtering, Read mapping, Visualisation, Taxonomic classification, Cross-assembly, Sequencing quality control, Expression analysis, Statistical calculation	2024-07-15	2025-03-20	4	True	False	True	True	upload1, kraken2, est_abundance, recentrifuge, fastp, falco	UseGalaxy.eu, UseGalaxy.fr	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		1665	2226	2.783333	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	Sequence alignment analysis, Read mapping, Generation, Sequence composition calculation, Formatting, Genome indexing, Sequencing quality control, Sequence alignment, Variant calling, Statistical calculation, Data handling	2017-02-16	2024-03-15	23	True	False	False	True	picard_MergeSamFiles, vcffilter2, vcf2tsv, bwa_mem, Cut1, picard_MarkDuplicates, fastqc, freebayes, bamFilter, bamleftalign	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		8749	15635	2.100000	0