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 Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Statistical calculation, Genome assembly, Coding region prediction, Sequencing quality control, Genome annotation, Gene prediction, Aggregation, Sequence composition calculation, Validation, Visualisation, Sequence assembly validation 2017-10-11 2025-05-15 24 True True False True unicycler, multiqc, fastqc, prokka, quast UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2857850 7551800 4.516667 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 Statistical calculation, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence composition calculation, Read mapping, Visualisation, Sequence contamination filtering, Sequence assembly validation 2021-03-24 2025-03-20 16 True False True True shovill, upload1, fastqc, falco, bandage_info, fastp, bandage_image, quast UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 9861 15245 3.633333 0
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, Sequence visualisation, Read mapping, Genome visualisation 2018-06-14 2024-06-24 29 True False False True random_lines1, tp_sed_tool, tp_replace_in_line, circos_interval_to_tiles, collapse_dataset, bedtools_sortbed, tp_cat, circos, join1, tp_replace_in_column, bedtools_complementbed, circos_aln_to_links, tp_sort_header_tool, fasta_filter_by_length, lastz_wrapper_2, Grep1, mergeCols1, tp_grep_tool, datamash_ops, bedtools_intersectbed, jbrowse, upload1, addValue, Filter1, cat1, Cut1, fasta_compute_length 0 6714 12964 2.933333 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation 2025-10-19 2025-10-19 0 True False True True coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat UseGalaxy.cz, UseGalaxy.eu 0 1 2 0.000000 0
Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Statistical calculation, Sequence assembly validation, Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Sequencing error detection, Filtering, Sequencing quality control, Cross-assembly, Sequence alignment, Scatter plot plotting, Sequence composition calculation, Read mapping, Visualisation, De-novo assembly, Sequence contamination filtering, Mapping assembly 2021-03-24 2024-11-29 15 True False False True CONVERTER_bz2_to_uncompressed, bandage_image, bwa_mem2, upload1, fastqc, porechop, nanoplot, fastp, filtlong, polypolish, flye, quast UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 10187 15281 3.416667 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification 2024-03-04 2024-06-27 4 True False False True recentrifuge, upload1, kraken2, est_abundance UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 813 1091 3.350000 0
Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2025-06-04 12 True False False True interactive_tool_rstudio, raxml, upload1 UseGalaxy.eu 0 2167 3129 2.266667 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 Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2022-03-16 2025-05-26 13 True False False True tb_variant_filter, tp_sed_tool, tp_replace_in_line, clustering_from_distmat, collapse_dataset, tp_cat, trimmomatic, snp_dists, samtools_view, snippy, snp_sites, bcftools_consensus, tp_easyjoin_tool, Grep1, tp_grep_tool, __MERGE_COLLECTION__, upload1, tb_profiler_profile, addName UseGalaxy.eu 0 2657 3823 2.833333 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2025-03-14 2025-03-14 1 True False False False fasttree, upload1 GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi 0 81 102 3.966667 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, Coding region prediction, Genome visualisation 2018-03-06 2025-03-19 26 True True True True prokka, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2863372 7560948 4.366667 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 create_or_update, jbrowse, iframe, create_account, list_organism UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2619764 6752999 5.116667 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 Antimicrobial resistance prediction, Read mapping, Genome annotation, Genome visualisation 2024-01-23 2025-06-10 9 True False True True jbrowse, upload1, tbl2gff3, staramr_search, Grep1, bakta, bowtie2 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.org (Main) 0 3221 4425 2.950000 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 Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Scaffolding, Structural variation detection 2024-02-01 2024-10-15 6 True False True True Grouping1, jbrowse, upload1, tp_replace_in_column, isescan, tp_tail_tool, tbl2gff3, bakta, integron_finder, plasmidfinder UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) 0 5939 7985 2.550000 0
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 composition calculation, Genome comparison, Validation, Sequencing quality control, Sequence assembly validation 2025-03-14 2025-03-14 1 True False False False drep_dereplicate, checkm2, upload1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 67 74 2.916667 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, Remove beginning1, bg_uniq, cat1, Cut1, datasets_download_genome, sort1 UseGalaxy.fr UseGalaxy.cz 0 67 80 3.366667 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 De-novo assembly, Database search, Coding region prediction, Sequence alignment analysis, Transcriptome assembly, Phylogenetic tree generation, Multiple sequence alignment 2022-09-08 2025-06-03 10 True False False True join1, bg_diamond, tp_split_on_column, collapse_dataset, tab2fasta, Filter1, Add_a_column1, regexColumn1, rapidnj, cat1, Cut1, orfipy, gops_intersect_1, rbc_mafft, bg_diamond_makedb, bg_diamond_view UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1792 2538 3.100000 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Transposon prediction, Sequence trimming, Primer removal, Read pre-processing 2019-07-02 2024-03-18 12 True True False True cutadapt, tp_easyjoin_tool, gff_to_prot, bowtie_wrapper, Filter1, Add_a_column1, transit_gumbel, Cut1, tp_sort_header_tool, deeptools_bam_coverage, bg_find_subsequences, __EXTRACT_DATASET__ UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 2852966 7544276 4.200000 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 Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2018-02-26 2025-03-19 24 True False False True snippy, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 14933 23903 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 Phylogenetic analysis, DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Visualisation 2017-06-22 2024-08-09 4 True False False True mothur_screen_seqs, mothur_make_group, mothur_classify_otu, metaphlan2, mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, metaphlan2krona, mothur_merge_files, mothur_align_seqs, humann2_renorm_table, humann2, mothur_make_shared, krona-text, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, humann2_regroup_table, taxonomy_krona_chart, mothur_cluster_split, mothur_filter_seqs UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 7951 10780 2.716667 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 Statistical calculation, Phylogenetic tree editing, Sequence alignment analysis, Phylogenetic analysis, Phylogenetic tree visualisation, Primer removal, Sequence trimming, Sequencing quality control, Taxonomic classification, Conversion, Sequence composition calculation, Read pre-processing, Validation, Visualisation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference 2020-02-13 2025-06-16 6 True False True True metaphlan, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan2_humann2, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 691 881 2.300000 0
Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Analysis, Visualisation, Deposition, DNA barcoding, Variant calling 2024-06-05 2025-07-03 11 True False True True dada2_makeSequenceTable, Grouping1, tp_replace_in_line, dada2_filterAndTrim, Add_a_column1, tp_replace_in_column, phyloseq_from_dada2, __SORTLIST__, dada2_plotQualityProfile, interactive_tool_phyloseq, dada2_dada, dada2_removeBimeraDenovo, dada2_learnErrors, dada2_assignTaxonomyAddspecies, __UNZIP_COLLECTION__, dada2_mergePairs, collection_element_identifiers, tp_head_tool, dada2_seqCounts, cat1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 6280 8875 2.383333 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 Statistical calculation, Genome annotation, Aggregation, Visualisation, Taxonomic classification 2023-05-03 2025-04-24 6 True False True True interactive_tool_pavian, metaphlan, interactive_tool_phinch, krakentools_kreport2krona, taxonomy_krona_chart, kraken2, est_abundance, __UNZIP_COLLECTION__, kraken_biom UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 11417 15283 2.016667 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, Sequence composition calculation, Validation, Visualisation, Sequencing quality control, Taxonomic classification 2020-11-24 2024-07-31 5 True False False True multiqc, fastqc, tp_replace_in_line, porechop, datamash_reverse, Remove beginning1, taxonomy_krona_chart, kraken2, fastp UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 7623 10518 2.600000 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 Genome assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Sequence assembly visualisation, Box-Whisker plot plotting, Data handling, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Variant calling, Taxonomic classification, Scatter plot plotting, Aggregation, Phylogenetic tree reconstruction, Validation, Visualisation, De-novo assembly, Mapping assembly, Sequence assembly, Statistical calculation, Mapping, Sequence alignment analysis, Antimicrobial resistance prediction, Sequencing quality control, Multiple sequence alignment, Base-calling, Phylogenetic tree analysis, Multilocus sequence typing, Sequence composition calculation, Cross-assembly, Pairwise sequence alignment, Sequence contamination filtering 2023-01-26 2024-09-27 11 True False True True Grouping1, tp_sorted_uniq, param_value_from_file, porechop, snpSift_filter, tp_multijoin_tool, collapse_dataset, tab2fasta, Add_a_column1, split_file_to_collection, snpSift_extractFields, tp_find_and_replace, fasta_merge_files_and_filter_unique_sequences, flye, __FILTER_FAILED_DATASETS__, Count1, tp_cut_tool, barchart_gnuplot, bcftools_norm, medaka_consensus_pipeline, multiqc, bedtools_getfastabed, tp_replace_in_column, bamtools_split_mapped, table_compute, abricate, Remove beginning1, kraken2, minimap2, nanoplot, samtools_coverage, samtools_fastx, fasttree, compose_text_param, bcftools_consensus, regex1, krakentools_kreport2krona, regexColumn1, clair3, Grep1, Paste1, __BUILD_LIST__, clustalw, newick_display, __FILTER_EMPTY_DATASETS__, krakentools_extract_kraken_reads, mlst, tp_split_on_column, collection_element_identifiers, fastqc, tp_head_tool, CONVERTER_gz_to_uncompressed, samtools_depth, taxonomy_krona_chart, ggplot2_heatmap, fastp, Cut1, collection_column_join, bandage_image, add_line_to_file, fasta2tab UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 4630 6981 3.416667 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 Phylogenetic tree editing, Taxonomic classification, Aggregation, Validation, Visualisation, Read pre-processing, Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Phylogenetic analysis, Primer removal, Sequence trimming, Sequencing quality control, Conversion, Sequence composition calculation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference 2019-11-21 2025-06-16 6 True True True True metaphlan, Grouping1, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan_humann, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 2851586 7538037 4.316667 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation 2022-12-05 2025-06-16 6 True False True True coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat UseGalaxy.cz, UseGalaxy.eu 0 4120 5765 3.033333 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 Statistical calculation, Sequence contamination filtering, Aggregation, Sequence composition calculation, Visualisation, Sequencing quality control, Taxonomic classification 2022-09-29 2024-11-29 5 True False True True fastqc, porechop, krakentools_kreport2krona, Filter1, taxonomy_krona_chart, kraken2, fastp GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2502 3630 2.833333 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 Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Antimicrobial resistance prediction, Sequence analysis, De-novo assembly, Scatter plot plotting, Aggregation, Pairwise sequence alignment, Mapping assembly 2019-06-25 2024-06-14 4 True False True True unicycler, miniasm, racon, nanoplot, minimap2, staramr_search, bandage_image, gfa_to_fa, PlasFlow UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3096 4347 2.950000 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 0 520 812 2.916667 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Statistical calculation, Genome assembly, Sequence composition calculation, Validation, Sequencing quality control, Sequence assembly validation 2023-12-05 2025-05-15 6 True False True False checkm_lineage_wf, megahit GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main), UseGalaxy.org.au 0 5215 6400 1.533333 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 0 380 611 3.233333 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 analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation 2019-05-13 2024-06-14 5 True False True True mothur_screen_seqs, mothur_remove_lineage, mothur_classify_otu, collapse_dataset, mothur_unique_seqs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4951 8234 4.600000 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 analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation 2017-02-12 2024-03-14 4 True False False True mothur_screen_seqs, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_get_groups, mothur_classify_otu, mothur_unique_seqs, mothur_make_contigs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_align_seqs, mothur_seq_error, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, mothur_dist_seqs, taxonomy_krona_chart, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 11419 16756 2.766667 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 Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Antimicrobial resistance prediction, Phylogenetic tree generation, Sequencing quality control, Taxonomic classification, Variant calling, Sequence analysis, Genome visualisation, Local alignment, Sequence alignment, Global alignment, Sequence composition calculation, Validation, Sequence contamination filtering 2020-07-25 2024-07-26 30 True False True True tb_variant_filter, tp_sed_tool, mosdepth, samtools_stats, qualimap_bamqc, multiqc, kraken2, jvarkit_wgscoverageplotter, snippy, bcftools_consensus, EMBOSS:%20seqret84, tp_awk_tool, EMBOSS: seqret84, tbvcfreport, jbrowse, upload1, fastqc, tb_profiler_profile, fastp, __FLATTEN__ 0 7388 11435 3.016667 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 438 576 2.366667 0
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, Visualisation, Filtering, Prediction and recognition 2020-10-16 2024-03-14 20 True False False True msconvert, tp_replace_in_column, tp_replace_in_line, regex1, query_tabular, Remove beginning1, Filter1, peptide_shaker, unipept, flashlfq, Cut1, search_gui, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 879 1492 3.800000 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 408 579 4.233333 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 query_tabular, sqlite_to_tabular, unipept, search_gui, peptide_shaker UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 2867 4572 2.716667 0
Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Sequencing quality control, Taxonomic classification, Cross-assembly, Read mapping, Visualisation, Sequence contamination filtering 2024-07-15 2025-03-20 4 True False True True upload1, falco, kraken2, fastp, est_abundance, recentrifuge UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.org (Main) 0 1487 1934 2.850000 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 Statistical calculation, Generation, Sequence alignment analysis, Genome indexing, Data handling, Sequencing quality control, Variant calling, Formatting, Sequence alignment, Sequence composition calculation, Read mapping 2017-02-16 2024-03-15 23 True False False True picard_MarkDuplicates, bwa_mem, fastqc, bamleftalign, vcffilter2, bamFilter, vcf2tsv, picard_MergeSamFiles, Cut1, freebayes UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 8501 15358 2.150000 0