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	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Formatting, Read mapping, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Primer removal, Local alignment, Sequence assembly visualisation, Sequence composition calculation, Sequencing quality control, Read pre-processing, Sequence assembly validation, Sequence file editing, Sequence alignment analysis, Variant calling, Sequence trimming	2026-03-24	2026-03-24	0	True	False	True	True	coverm_contig, metaspades, bamtools, fastqc, bandage_image, random_lines1, bg_uniq, megahit, ngsutils_bam_filter, megahit_contig2fastg, quast, cutadapt, bowtie2, seqtk_subseq, tp_cat, filter_tabular, collection_column_join, bandage_info		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)	5	6	0.450000
Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Gene prediction, Genome annotation, Aggregation, Genome assembly, Sequence composition calculation, Sequencing quality control, Validation, Visualisation, Statistical calculation, Sequence assembly validation, Coding region prediction	2017-10-11	2026-01-23	25	True	True	False	True	multiqc, fastqc, prokka, quast, unicycler	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3594287	8664791	7.133333
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	Read mapping, Sequencing error detection, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Sequence alignment, Box-Whisker plot plotting, Mapping assembly, Sequence assembly visualisation, De-novo assembly, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Cross-assembly, Filtering, Scatter plot plotting	2021-03-24	2026-01-05	16	True	False	False	True	fastqc, bandage_image, bwa_mem2, filtlong, polypolish, nanoplot, __FLATTEN__, fastp, CONVERTER_bz2_to_uncompressed, porechop, __EXTRACT_DATASET__, quast, upload1, flye	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr	11108	16515	7.600000
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	Read mapping, Sequence assembly visualisation, Genome assembly, Visualisation, Sequencing quality control, Sequence assembly validation, Sequence contamination filtering	2021-03-24	2026-01-05	18	True	False	True	True	bandage_image, falco, quast, fastp, shovill, upload1, bandage_info	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		11060	16854	9.533333
Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence alignment, Mapping, Read mapping, Sequence visualisation, Genome visualisation	2018-06-14	2024-06-24	29	True	False	False	True	tp_sed_tool, random_lines1, tp_sort_header_tool, upload1, mergeCols1, jbrowse, lastz_wrapper_2, tp_replace_in_line, addValue, circos_interval_to_tiles, Cut1, datamash_ops, fasta_compute_length, bedtools_intersectbed, tp_grep_tool, cat1, join1, tp_replace_in_column, bedtools_complementbed, bedtools_sortbed, circos, fasta_filter_by_length, circos_aln_to_links, Filter1, tp_cat, collapse_dataset, Grep1			6877	13146	8.050000
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, Taxonomic classification, Expression analysis, Cross-assembly	2024-03-04	2025-12-18	5	True	False	False	True	est_abundance, recentrifuge, kraken2, upload1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main)	987	1320	8.450000
Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Antimicrobial resistance prediction, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2022-03-16	2025-05-26	13	True	False	False	True	tp_sed_tool, upload1, tp_replace_in_line, trimmomatic, samtools_view, __MERGE_COLLECTION__, snippy, snp_dists, tb_variant_filter, tp_grep_tool, clustering_from_distmat, tp_easyjoin_tool, tb_profiler_profile, bcftools_consensus, tp_cat, snp_sites, addName, collapse_dataset, Grep1	UseGalaxy.eu		3364	4803	7.783333
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		2413	3446	7.766667
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	upload1, fasttree	Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	GalaxyTrakr	152	177	8.533333
Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Gene prediction, Genome annotation, Coding region prediction, Genome visualisation	2018-03-06	2026-01-23	27	True	True	True	True	prokka, jbrowse	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3600357	8674742	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	create_or_update, create_account, iframe, jbrowse, list_organism	UseGalaxy.be	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	3356097	7865909	13.083333
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	bakta, staramr_search, tbl2gff3, bowtie2, upload1, jbrowse, Grep1	Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org (Main)	4031	5464	9.283333
Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Protein feature detection, Genome assembly, Genome visualisation, Scaffolding, Multilocus sequence typing, Structural variation detection, Nucleic acid feature detection, Sequence motif recognition	2024-02-01	2024-10-15	6	True	False	True	True	bakta, integron_finder, tp_tail_tool, Grouping1, isescan, tbl2gff3, upload1, plasmidfinder, tp_replace_in_column, jbrowse	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	7722	10549	7.716667
Genome Annotation	Bacterial genome quality control	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html	Genomics, Microbiology	Statistical calculation, Sequence assembly validation, Sequence composition calculation, Sequencing quality control, Validation, Genome comparison	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	159	193	6.666667
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 retrieval, Sequence database search, Data handling	2025-03-14	2025-03-14	1	True	False	False	False	sort1, bg_uniq, cat1, Remove beginning1, Cut1, upload1, datasets_download_genome	UseGalaxy.fr	UseGalaxy.cz	100	118	8.133333
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, Database search, Coding region prediction, De-novo assembly, Phylogenetic tree generation, Transcriptome assembly, Multiple sequence alignment	2022-09-08	2025-06-03	10	True	False	False	True	tab2fasta, bg_diamond, bg_diamond_view, regexColumn1, cat1, Add_a_column1, Cut1, Filter1, join1, tp_split_on_column, rapidnj, rbc_mafft, bg_diamond_makedb, collapse_dataset, gops_intersect_1, orfipy	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	1995	2761	9.716667
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, Transposon prediction, Read pre-processing, Sequence trimming	2019-07-02	2024-03-18	12	True	True	False	True	transit_gumbel, gff_to_prot, bowtie_wrapper, bg_find_subsequences, Cut1, Filter1, tp_easyjoin_tool, tp_sort_header_tool, __EXTRACT_DATASET__, cutadapt, deeptools_bam_coverage, Add_a_column1	UseGalaxy.org.au, UseGalaxy.no	UseGalaxy.cz, UseGalaxy.eu	3589581	8657681	5.766667
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	Genome visualisation, Phylogenetic tree visualisation, Variant calling, 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	15751	24927	4.900000
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	Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding	2017-06-22	2024-08-09	4	True	False	False	True	humann2_renorm_table, mothur_unique_seqs, mothur_make_shared, humann2, mothur_make_biom, metaphlan2, humann2_regroup_table, mothur_merge_files, mothur_pre_cluster, mothur_filter_seqs, mothur_make_group, metaphlan2krona, mothur_screen_seqs, mothur_count_seqs, taxonomy_krona_chart, mothur_classify_otu, mothur_classify_seqs, krona-text, mothur_summary_seqs, mothur_cluster_split, mothur_align_seqs		UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no	10070	13697	5.916667
Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Formatting, Read mapping, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Primer removal, Local alignment, Sequence assembly visualisation, Sequence composition calculation, Sequencing quality control, Read pre-processing, Sequence assembly validation, Sequence file editing, Sequence alignment analysis, Variant calling, Sequence trimming	2022-12-05	2025-12-08	8	True	False	True	True	coverm_contig, metaspades, bamtools, fastqc, bandage_image, random_lines1, bg_uniq, megahit, ngsutils_bam_filter, megahit_contig2fastg, quast, cutadapt, bowtie2, seqtk_subseq, tp_cat, filter_tabular, collection_column_join, bandage_info		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)	4987	6864	10.016667
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	Species frequency estimation, Visualisation, Sequence similarity search, Sequence comparison, Statistical calculation, Primer removal, Conversion, Taxonomic classification, Phylogenetic tree visualisation, Phylogenetic tree editing, Phylogenetic analysis, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Sequence alignment analysis, Phylogenetic inference, Sequence trimming	2020-02-13	2025-06-16	6	True	False	True	True	multiqc, fastqc, tp_find_and_replace, tp_sort_header_tool, fastq_paired_end_interlacer, metaphlan, bg_sortmerna, Cut1, export2graphlan, humann_regroup_table, humann_renorm_table, humann_split_stratified_table, humann, graphlan, taxonomy_krona_chart, combine_metaphlan2_humann2, graphlan_annotate, humann_rename_table, humann_unpack_pathways, cutadapt, Grep1	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.no	930	1194	9.900000
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	Deposition, Analysis, Variant calling, DNA barcoding, Visualisation	2024-06-05	2025-07-03	11	True	False	True	True	dada2_removeBimeraDenovo, phyloseq_from_dada2, dada2_assignTaxonomyAddspecies, interactive_tool_phyloseq, __SORTLIST__, tp_replace_in_line, Grouping1, dada2_filterAndTrim, dada2_makeSequenceTable, dada2_dada, __UNZIP_COLLECTION__, dada2_seqCounts, cat1, tp_head_tool, collection_element_identifiers, Add_a_column1, tp_replace_in_column, dada2_plotQualityProfile, dada2_learnErrors, dada2_mergePairs	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		8428	11998	5.416667
Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance	Mapping assembly, Sequence analysis, Sequence assembly visualisation, Genome assembly, Aggregation, De-novo assembly, Antimicrobial resistance prediction, Pairwise sequence alignment, Box-Whisker plot plotting, Scatter plot plotting	2019-06-25	2024-06-14	4	True	False	True	True	bandage_image, racon, nanoplot, staramr_search, minimap2, miniasm, unicycler, PlasFlow, gfa_to_fa	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	3836	5305	6.650000
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	Statistical calculation, Genome annotation, Taxonomic classification, Aggregation, Visualisation	2023-05-03	2025-12-18	7	True	False	True	True	interactive_tool_pavian, est_abundance, krakentools_kreport2krona, taxonomy_krona_chart, kraken_biom, kraken2, __UNZIP_COLLECTION__, metaphlan, interactive_tool_phinch	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		13774	18313	5.550000
Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Genome annotation, Read mapping, Sequence clustering, Sequence composition calculation, Sequence assembly, Sequencing quality control, Validation, Sequence assembly validation, Statistical calculation, Read binning, Genome comparison	2023-12-05	2026-03-18	8	True	False	True	True	Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, binette, concoct_extract_fasta_bins, semibin, metabat2, concoct, maxbin2, __BUILD_LIST__, checkm_lineage_wf, bowtie2, samtools_sort, das_tool, concoct_coverage_table, concoct_cut_up_fasta, drep_dereplicate, metabat2_jgi_summarize_bam_contig_depths	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org.au, UseGalaxy.org (Main)	6448	7876	5.450000
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	Aggregation, Species frequency estimation, Visualisation, Sequence comparison, Sequence similarity search, Statistical calculation, Primer removal, Conversion, Taxonomic classification, Phylogenetic tree visualisation, Phylogenetic tree editing, Phylogenetic analysis, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Sequence alignment analysis, Phylogenetic inference, Sequence trimming	2019-11-21	2025-06-16	6	True	True	True	True	multiqc, fastqc, tp_find_and_replace, tp_sort_header_tool, fastq_paired_end_interlacer, metaphlan, combine_metaphlan_humann, Grouping1, bg_sortmerna, Cut1, export2graphlan, humann_regroup_table, humann_renorm_table, humann_split_stratified_table, humann, graphlan, taxonomy_krona_chart, graphlan_annotate, humann_rename_table, humann_unpack_pathways, cutadapt, Grep1	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.eu	3588528	8652229	6.783333
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	Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Sequence composition calculation, Sequencing quality control, Sequence contamination filtering	2022-09-29	2024-11-29	5	True	False	True	True	fastqc, krakentools_kreport2krona, taxonomy_krona_chart, fastp, Filter1, porechop, kraken2	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	3217	4688	8.083333
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	Mapping, Phylogenetic tree generation (from molecular sequences), Aggregation, Genome assembly, Scatter plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Base-calling, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly, Taxonomic classification, Mapping assembly, Sequence assembly visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), De-novo assembly, Sequence composition calculation, Sequencing quality control, Validation, Multilocus sequence typing, Phylogenetic tree generation, Cross-assembly, Pairwise sequence alignment, Sequence alignment analysis, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Variant calling, Multiple sequence alignment	2023-01-26	2025-11-18	12	True	False	True	True	multiqc, fastqc, bandage_image, tp_find_and_replace, bamtools_split_mapped, __FILTER_EMPTY_DATASETS__, fasttree, tab2fasta, mlst, barchart_gnuplot, bcftools_norm, abricate, samtools_fastx, krakentools_kreport2krona, Grouping1, Count1, Cut1, __BUILD_LIST__, fastp, porechop, tp_cut_tool, Paste1, clair3, collection_column_join, fasta_merge_files_and_filter_unique_sequences, samtools_coverage, table_compute, param_value_from_file, compose_text_param, clustalw, snpSift_extractFields, CONVERTER_gz_to_uncompressed, tp_head_tool, __FILTER_FAILED_DATASETS__, tp_multijoin_tool, collection_element_identifiers, split_file_to_collection, tp_split_on_column, ggplot2_heatmap, kraken2, Add_a_column1, tp_replace_in_column, newick_display, regex1, samtools_depth, flye, add_line_to_file, fasta2tab, regexColumn1, taxonomy_krona_chart, bedtools_getfastabed, medaka_consensus_pipeline, Remove beginning1, nanoplot, snpSift_filter, minimap2, bcftools_consensus, tp_sorted_uniq, krakentools_extract_kraken_reads, collapse_dataset, Grep1	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz	5406	7938	8.483333
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, Taxonomic classification, Visualisation, Sequence composition calculation, Sequencing quality control, Validation, Sequence contamination filtering	2020-11-24	2024-07-31	5	True	False	False	True	datamash_reverse, multiqc, fastqc, tp_replace_in_line, taxonomy_krona_chart, Remove beginning1, fastp, porechop, kraken2	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	9371	12990	5.483333
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	466	761	9.766667
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	717	1072	6.933333
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 annotation, Sequence composition calculation, Sequencing quality control, Validation, Sequence assembly validation, Statistical calculation, Genome comparison, Data handling	2025-12-18	2025-12-18	1	True	False	False	False	bakta, multiqc, fasterq_dump, cat1, Grouping1, Summary_Statistics1, Remove beginning1, Cut1, tp_sort_header_tool, checkm_lineage_wf, __EXTRACT_DATASET__, join1, collection_column_join, drep_dereplicate, tp_replace_in_column, collapse_dataset	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.cz	592	827	5.533333
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	Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding, Phylogenetic tree generation, Phylogenetic tree reconstruction, Phylogenetic tree analysis	2019-05-13	2025-12-18	6	True	False	True	True	mothur_unique_seqs, XY_Plot_1, mothur_remove_lineage, mothur_make_shared, mothur_tree_shared, mothur_remove_seqs, mothur_count_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_pre_cluster, mothur_filter_seqs, mothur_summary_single, newick_display, mothur_dist_shared, mothur_screen_seqs, mothur_count_seqs, mothur_venn, mothur_classify_otu, mothur_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_heatmap_sim, mothur_summary_seqs, mothur_cluster_split, collapse_dataset, mothur_rarefaction_single, mothur_remove_groups	UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.fr	6325	10649	7.750000
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	Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding, Phylogenetic tree generation, Phylogenetic tree reconstruction, Phylogenetic tree analysis	2017-02-12	2025-12-18	5	True	False	False	True	mothur_unique_seqs, XY_Plot_1, mothur_remove_lineage, mothur_make_shared, mothur_tree_shared, mothur_remove_seqs, mothur_remove_groups, mothur_make_biom, mothur_count_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_pre_cluster, mothur_filter_seqs, mothur_summary_single, mothur_taxonomy_to_krona, newick_display, mothur_dist_shared, mothur_seq_error, mothur_screen_seqs, mothur_count_seqs, mothur_make_contigs, mothur_venn, taxonomy_krona_chart, mothur_classify_otu, mothur_classify_seqs, mothur_cluster, mothur_dist_seqs, mothur_heatmap_sim, mothur_summary_seqs, mothur_cluster_split, mothur_align_seqs, mothur_rarefaction_single, mothur_get_groups	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	13446	19857	4.983333
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	Taxonomic classification, Phylogenetic tree visualisation, Sequence analysis, Genome visualisation, Sequence composition calculation, Sequencing quality control, Validation, Sequence contamination filtering, Statistical calculation, Sequence alignment, Global alignment, Variant calling, Phylogenetic tree generation, Antimicrobial resistance prediction, Sequence alignment analysis, Local alignment	2020-07-25	2026-01-06	32	True	False	True	True	tp_sed_tool, fastqc, multiqc, EMBOSS: seqret84, upload1, jbrowse, samtools_stats, __FLATTEN__, EMBOSS:%20seqret84, fastp, snippy, tb_variant_filter, jvarkit_wgscoverageplotter, tp_awk_tool, kraken2, mosdepth, tbvcfreport, qualimap_bamqc, tb_profiler_profile, bcftools_consensus			8191	12417	7.666667
Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation	2017-06-28	2024-06-14	41	True	False	True	True	search_gui, sqlite_to_tabular, query_tabular, peptide_shaker, unipept	UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.be, UseGalaxy.cz	3044	4795	9.550000
Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Query and retrieval, Indexing, Principal component visualisation, Visualisation, Quantification, Differential protein expression analysis, Statistical inference, Heat map generation, Filtering, Functional clustering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_sample, metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	443	615	15.016667
Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Formatting, Label-free quantification, Prediction and recognition, Filtering, Visualisation	2020-10-16	2024-03-14	20	True	False	False	True	search_gui, flashlfq, tp_replace_in_line, msconvert, Remove beginning1, Cut1, query_tabular, Filter1, peptide_shaker, tp_replace_in_column, unipept, regex1, Grep1	UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no	924	1541	9.083333
Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Query and retrieval, Indexing, Principal component visualisation, Visualisation, Quantification, Differential protein expression analysis, Statistical inference, Heat map generation, Filtering, Functional clustering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_sample, metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	472	612	14.383333
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	Taxonomic classification, Read mapping, Visualisation, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Cross-assembly, Expression analysis	2024-07-15	2025-12-18	5	True	False	True	True	est_abundance, falco, fastp, upload1, kraken2, recentrifuge	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)		1934	2590	10.616667
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, Read mapping, Generation, Genome indexing, Sequence composition calculation, Sequencing quality control, Statistical calculation, Sequence alignment, Sequence alignment analysis, Variant calling, Data handling	2017-02-16	2024-03-15	23	True	False	False	True	fastqc, bamFilter, bamleftalign, picard_MergeSamFiles, vcf2tsv, Cut1, freebayes, bwa_mem, picard_MarkDuplicates, vcffilter2	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no	9674	16666	5.516667