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	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence visualisation, Read mapping, Mapping, Sequence alignment, Genome visualisation	2018-06-14	2026-04-13	30	True	False	False	True	jbrowse, cat1, collapse_dataset, tp_replace_in_column, random_lines1, tp_replace_in_line, join1, fasta_filter_by_length, circos_interval_to_tiles, tp_sort_header_tool, Filter1, fasta_compute_length, addValue, tp_cat, bedtools_intersectbed, circos, tp_sed_tool, datamash_ops, tp_grep_tool, mergeCols1, Cut1, bedtools_sortbed, upload1, Grep1, circos_aln_to_links, lastz_wrapper_2, bedtools_complementbed			6969	13261	8.116667
Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Statistical calculation, Genome assembly, Coding region prediction, Visualisation, Sequence assembly validation, Validation, Gene prediction, Sequence composition calculation, Aggregation, Genome annotation, Sequencing quality control	2017-10-11	2026-01-23	25	True	True	False	True	multiqc, fastqc, unicycler, quast, prokka	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3823772	9058168	7.083333
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 assembly visualisation, Read mapping, Genome assembly, Visualisation, Sequence assembly validation, Sequence contamination filtering, Sequencing quality control	2021-03-24	2026-01-05	18	True	False	True	True	upload1, shovill, bandage_image, fastp, bandage_info, quast, falco	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		11568	17594	9.533333
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, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control	2026-05-21	2026-05-21	0	True	False	True	True	metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	6	7	11.666667
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	Scatter plot plotting, De-novo assembly, Sequence assembly visualisation, Statistical calculation, Genome assembly, Sequencing error detection, Read mapping, Visualisation, Filtering, Sequence assembly validation, Sequence alignment, Box-Whisker plot plotting, Sequence composition calculation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control	2021-03-24	2026-01-05	16	True	False	False	True	upload1, bandage_image, nanoplot, porechop, filtlong, fastqc, flye, __EXTRACT_DATASET__, fastp, polypolish, quast, __FLATTEN__, CONVERTER_bz2_to_uncompressed, bwa_mem2	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr	11438	16929	7.583333
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, Expression analysis, Taxonomic classification, Statistical calculation	2024-03-04	2026-04-08	6	True	False	False	True	recentrifuge, upload1, kraken2, est_abundance	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main)	1036	1378	8.266667
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, raxml, interactive_tool_rstudio	UseGalaxy.eu		2502	3565	8.050000
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 visualisation, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree generation	2022-03-16	2025-05-26	13	True	False	False	True	addName, __MERGE_COLLECTION__, trimmomatic, collapse_dataset, tp_replace_in_line, snippy, samtools_view, tp_cat, tp_sed_tool, tb_variant_filter, bcftools_consensus, snp_sites, tp_grep_tool, tb_profiler_profile, upload1, Grep1, clustering_from_distmat, snp_dists, tp_easyjoin_tool	UseGalaxy.eu		3555	5077	7.800000
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	198	239	10.266667
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, Gene prediction, Genome annotation, Genome visualisation	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.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3829962	9068268	7.166667
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, list_organism, create_account, create_or_update		UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	3585787	8259740	13.183333
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	Protein feature detection, Structural variation detection, Genome assembly, Scaffolding, Multilocus sequence typing, Genome visualisation, Nucleic acid feature detection, Sequence motif recognition, Genome annotation	2024-02-01	2024-10-15	6	True	False	True	True	isescan, upload1, Grouping1, plasmidfinder, integron_finder, tbl2gff3, jbrowse, tp_tail_tool, tp_replace_in_column, bakta	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main)	8485	11611	7.716667
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	upload1, Grep1, tbl2gff3, jbrowse, bowtie2, staramr_search, bakta	Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main)	4294	5838	9.300000
Genome Annotation	Bacterial genome quality control	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html	Genomics, Microbiology	Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Sequence assembly validation, Sequencing quality control	2025-03-14	2025-03-14	1	True	False	False	False	checkm2, drep_dereplicate, upload1	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz	195	233	7.733333
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	2026-04-13	2	True	False	False	False	upload1, sort1, Remove beginning1, cat1, Cut1, datasets_download_genome, bg_uniq	UseGalaxy.fr	UseGalaxy.cz	115	133	11.683333
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, Multiple sequence alignment, Database search, De-novo assembly, Transcriptome assembly, Coding region prediction, Phylogenetic tree generation	2022-09-08	2025-06-03	10	True	False	False	True	bg_diamond_makedb, gops_intersect_1, bg_diamond_view, tp_split_on_column, bg_diamond, Filter1, cat1, Add_a_column1, orfipy, tab2fasta, rbc_mafft, collapse_dataset, Cut1, rapidnj, regexColumn1, join1	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	2056	2827	9.833333
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, Sequence trimming, Transposon prediction, Read pre-processing	2019-07-02	2024-03-18	12	True	True	False	True	transit_gumbel, __EXTRACT_DATASET__, tp_sort_header_tool, Filter1, Add_a_column1, gff_to_prot, Cut1, deeptools_bam_coverage, tp_easyjoin_tool, cutadapt, bowtie_wrapper, bg_find_subsequences	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.no	UseGalaxy.cz, UseGalaxy.eu	3819196	9051236	5.700000
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	2026-01-23	25	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	16133	25453	5.000000
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	Phylogenetic analysis, Taxonomic classification, Sequencing quality control, Visualisation, Sequence read processing, Sequence clustering, DNA barcoding	2017-06-22	2024-08-09	4	True	False	False	True	mothur_filter_seqs, humann2_renorm_table, mothur_pre_cluster, humann2, mothur_cluster_split, metaphlan2, mothur_align_seqs, mothur_screen_seqs, mothur_make_biom, mothur_make_group, mothur_classify_otu, mothur_make_shared, mothur_summary_seqs, taxonomy_krona_chart, krona-text, mothur_merge_files, metaphlan2krona, mothur_unique_seqs, mothur_classify_seqs, humann2_regroup_table, mothur_count_seqs		UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no	11137	14970	5.733333
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 tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Read pre-processing, Sequence trimming, Sequencing quality control	2020-02-13	2025-06-16	6	True	False	True	True	graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, fastqc, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, combine_metaphlan2_humann2, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.no	1036	1323	9.983333
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	Taxonomic classification, Aggregation, Statistical calculation, Visualisation, Genome annotation	2023-05-03	2026-05-11	8	True	False	True	True	taxonomy_krona_chart, interactive_tool_phinch, est_abundance, kraken_biom, metaphlan, __UNZIP_COLLECTION__, krakentools_kreport2krona, interactive_tool_pavian, kraken2	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		14694	19544	5.583333
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, De-novo assembly, Sequence assembly visualisation, Sequence analysis, Genome assembly, Pairwise sequence alignment, Antimicrobial resistance prediction, Box-Whisker plot plotting, Aggregation, Mapping assembly	2019-06-25	2024-06-14	4	True	False	True	True	PlasFlow, bandage_image, nanoplot, miniasm, unicycler, racon, staramr_search, gfa_to_fa, minimap2	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	4171	5713	6.783333
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 contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Visualisation, Sequencing quality control	2020-11-24	2024-07-31	5	True	False	False	True	taxonomy_krona_chart, porechop, datamash_reverse, multiqc, Remove beginning1, fastqc, fastp, tp_replace_in_line, kraken2	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr	10045	13873	5.433333
Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Read mapping, Statistical calculation, Sequencing quality control, Sequence assembly validation, Read binning, Validation, Genome comparison, Sequence composition calculation, Sequence clustering, Genome annotation, Sequence assembly	2023-12-05	2026-04-09	9	True	False	True	True	concoct, concoct_cut_up_fasta, __BUILD_LIST__, Fasta_to_Contig2Bin, concoct_coverage_table, das_tool, metabat2_jgi_summarize_bam_contig_depths, bowtie2, samtools_sort, drep_dereplicate, maxbin2, metabat2, concoct_merge_cut_up_clustering, semibin, binette, checkm_lineage_wf, concoct_extract_fasta_bins	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main)	7203	8810	5.333333
Microbiome	Remove contamination and host reads	https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html		Validation, Sequencing quality control, Read mapping	2025-12-18	2026-05-12	3	True	False	True	True	bowtie2, __ZIP_COLLECTION__, multiqc	Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	GalaxyTrakr, MISSISSIPPI, UseGalaxy.no	355	431	6.166667
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 tree visualisation, Statistical calculation, Primer removal, Phylogenetic inference, Visualisation, Species frequency estimation, Sequence composition calculation, Sequence comparison, Phylogenetic tree editing, Phylogenetic analysis, Taxonomic classification, Conversion, Validation, Sequence similarity search, Aggregation, Read pre-processing, Sequence trimming, Sequencing quality control	2019-11-21	2025-06-16	6	True	True	True	True	graphlan_annotate, tp_find_and_replace, graphlan, multiqc, bg_sortmerna, tp_sort_header_tool, export2graphlan, cutadapt, fastq_paired_end_interlacer, Grouping1, fastqc, combine_metaphlan_humann, Cut1, humann_renorm_table, humann, Grep1, taxonomy_krona_chart, metaphlan, humann_rename_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.eu	3818338	9046054	6.816667
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, Deposition, Visualisation, Variant calling, DNA barcoding	2024-06-05	2026-04-13	12	True	False	True	True	dada2_plotQualityProfile, dada2_mergePairs, cat1, tp_replace_in_column, tp_replace_in_line, __UNZIP_COLLECTION__, tp_head_tool, phyloseq_from_dada2, Grouping1, dada2_makeSequenceTable, __SORTLIST__, dada2_removeBimeraDenovo, collection_element_identifiers, dada2_assignTaxonomyAddspecies, dada2_filterAndTrim, Add_a_column1, dada2_seqCounts, interactive_tool_phyloseq, dada2_dada, dada2_learnErrors	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		9282	13212	5.466667
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, Primer removal, Genome assembly, Visualisation, Local alignment, Sequence composition calculation, Formatting, Variant calling, Sequence file editing, Sequence assembly visualisation, Read mapping, Sequence assembly validation, Data handling, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequencing quality control	2022-12-05	2026-05-11	11	True	False	True	True	metaspades, collection_column_join, bandage_image, filter_tabular, coverm_contig, megahit_contig2fastg, bamtools, fastqc, bandage_info, megahit, bowtie2, tp_cat, quast, ngsutils_bam_filter, seqtk_subseq, random_lines1, cutadapt, bg_uniq		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	5414	7491	10.150000
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, Sequence composition calculation, Aggregation, Statistical calculation, Taxonomic classification, Visualisation, Sequencing quality control	2022-09-29	2024-11-29	5	True	False	True	True	taxonomy_krona_chart, porechop, fastqc, Filter1, fastp, krakentools_kreport2krona, kraken2	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3449	5021	8.383333
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, Statistical calculation, Genome assembly, Visualisation, Antimicrobial resistance prediction, Mapping, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Box-Whisker plot plotting, Sequence composition calculation, Phylogenetic tree generation (from molecular sequences), Base-calling, Phylogenetic tree analysis, Variant calling, Sequence assembly, Phylogenetic tree reconstruction, Phylogenetic tree generation, Scatter plot plotting, De-novo assembly, Taxonomic classification, Sequence assembly visualisation, Pairwise sequence alignment, Multilocus sequence typing, Data handling, Validation, Multiple sequence alignment, Aggregation, Cross-assembly, Mapping assembly, Sequence contamination filtering, Sequencing quality control	2023-01-26	2025-11-18	12	True	False	True	True	ggplot2_heatmap, Count1, Paste1, tp_find_and_replace, abricate, multiqc, fastp, table_compute, collapse_dataset, barchart_gnuplot, tp_replace_in_column, compose_text_param, minimap2, regexColumn1, mlst, __FILTER_FAILED_DATASETS__, CONVERTER_gz_to_uncompressed, __BUILD_LIST__, clair3, tp_split_on_column, krakentools_extract_kraken_reads, bamtools_split_mapped, samtools_fastx, tab2fasta, krakentools_kreport2krona, tp_head_tool, bedtools_getfastabed, fasta_merge_files_and_filter_unique_sequences, medaka_consensus_pipeline, Grouping1, split_file_to_collection, bcftools_consensus, tp_cut_tool, __FILTER_EMPTY_DATASETS__, samtools_coverage, snpSift_filter, Remove beginning1, fastqc, flye, fasta2tab, newick_display, regex1, Cut1, snpSift_extractFields, bcftools_norm, Grep1, tp_multijoin_tool, param_value_from_file, taxonomy_krona_chart, bandage_image, collection_element_identifiers, fasttree, nanoplot, tp_sorted_uniq, porechop, Add_a_column1, add_line_to_file, clustalw, samtools_depth, collection_column_join, kraken2	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz	5672	8267	8.566667
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	Data handling, Validation, Genome comparison, Sequence composition calculation, Statistical calculation, Genome annotation, Sequence assembly validation, Sequencing quality control	2025-12-18	2026-05-18	6	True	False	True	False	Summary_Statistics1, Grouping1, multiqc, Remove beginning1, __EXTRACT_DATASET__, tp_sort_header_tool, checkm_lineage_wf, cat1, fasterq_dump, drep_dereplicate, collapse_dataset, Cut1, kmetashot, tp_replace_in_column, collection_column_join, join1, bakta	UseGalaxy.eu		1022	1315	5.666667
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	518	857	10.133333
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	2026-02-18	2	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	771	1141	7.250000
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 analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding	2017-02-12	2025-12-18	5	True	False	False	True	mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_align_seqs, mothur_sub_sample, mothur_screen_seqs, mothur_taxonomy_to_krona, mothur_make_biom, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_get_groups, mothur_summary_seqs, mothur_venn, taxonomy_krona_chart, mothur_seq_error, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_make_contigs, mothur_remove_seqs, mothur_heatmap_sim	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	14146	20833	5.016667
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 analysis, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree generation, Sequence read processing, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence clustering, DNA barcoding	2019-05-13	2025-12-18	6	True	False	True	True	mothur_dist_shared, mothur_filter_seqs, mothur_count_seqs, mothur_tree_shared, mothur_rarefaction_single, mothur_dist_seqs, mothur_summary_single, collapse_dataset, mothur_chimera_vsearch, XY_Plot_1, mothur_pre_cluster, mothur_cluster, mothur_cluster_split, mothur_sub_sample, mothur_screen_seqs, mothur_remove_groups, mothur_classify_otu, mothur_count_groups, mothur_make_shared, newick_display, mothur_summary_seqs, mothur_venn, mothur_remove_lineage, mothur_unique_seqs, mothur_classify_seqs, mothur_remove_seqs, mothur_heatmap_sim	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.fr	6699	11212	7.700000
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, Phylogenetic tree visualisation, Taxonomic classification, Sequence analysis, Statistical calculation, Sequence alignment, Global alignment, Genome visualisation, Local alignment, Antimicrobial resistance prediction, Validation, Sequence composition calculation, Sequence contamination filtering, Variant calling, Sequencing quality control, Phylogenetic tree generation	2020-07-25	2026-01-06	32	True	False	True	True	kraken2, multiqc, jbrowse, qualimap_bamqc, fastp, samtools_stats, EMBOSS: seqret84, jvarkit_wgscoverageplotter, mosdepth, snippy, EMBOSS:%20seqret84, __FLATTEN__, tp_sed_tool, tb_variant_filter, bcftools_consensus, tp_awk_tool, fastqc, tb_profiler_profile, upload1, tbvcfreport			8399	12705	7.716667
Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Label-free quantification, Visualisation, Formatting, Filtering	2020-10-16	2024-03-14	20	True	False	False	True	Grep1, msconvert, peptide_shaker, Remove beginning1, flashlfq, query_tabular, Filter1, unipept, regex1, tp_replace_in_column, Cut1, tp_replace_in_line, search_gui	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no	937	1558	9.366667
Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Visualisation, Prediction and recognition	2017-06-28	2026-05-11	42	True	False	True	True	sqlite_to_tabular, query_tabular, unipept, peptide_shaker, search_gui	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3109	4879	9.833333
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, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	485	626	14.650000
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, Visualisation, Differential protein expression analysis, Principal component visualisation, Heat map generation, Quantification, Query and retrieval, Filtering, Indexing	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_viz, metaquantome_expand, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	452	626	15.466667
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	Expression analysis, Taxonomic classification, Statistical calculation, Read mapping, Visualisation, Cross-assembly, Sequence contamination filtering, Sequencing quality control	2024-07-15	2025-12-18	5	True	False	True	True	upload1, est_abundance, fastp, falco, recentrifuge, kraken2	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		2057	2730	10.500000
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, Statistical calculation, Read mapping, Generation, Data handling, Genome indexing, Sequence composition calculation, Sequence alignment, Formatting, Variant calling, Sequencing quality control	2017-02-16	2024-03-15	23	True	False	False	True	bamFilter, freebayes, bamleftalign, vcffilter2, picard_MarkDuplicates, fastqc, picard_MergeSamFiles, vcf2tsv, Cut1, bwa_mem	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no	9869	16898	5.550000