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 Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling 2024-08-18 2024-08-18 0 True False False True bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades UseGalaxy.cz, UseGalaxy.eu 0 2 2 0.100000 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 Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation 2021-03-24 2024-03-13 14 True False False True nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop UseGalaxy.eu UseGalaxy.cz 0 6851 10571 3.433333 0
Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Genome assembly, Statistical calculation 2021-03-24 2024-03-13 14 True False False True fastp, shovill, quast, fastqc, bandage_info, bandage_image, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no 0 6432 10369 3.750000 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation 2018-06-14 2024-06-24 29 True False False True circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1 0 5938 12067 3.033333 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Visualisation, Sequencing quality control, Genome annotation, Sequence assembly validation, Sequence composition calculation, Coding region prediction, Validation, Genome assembly, Gene prediction, Statistical calculation, Aggregation 2017-10-11 2024-03-13 23 True True False True multiqc, quast, prokka, fastqc, unicycler UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, HyPhy HIV NGS Tools, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2074750 5746521 4.550000 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation 2024-03-04 2024-06-27 4 True False False True est_abundance, upload1, kraken2, recentrifuge UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 229 302 3.950000 0
Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction 2022-03-16 2024-07-12 12 True False False True Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 1533 2414 3.133333 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 2024-03-12 11 True False False True interactive_tool_rstudio, upload1, raxml UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 0 1308 1983 2.183333 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 visualisation, Genome annotation, Gene prediction, Coding region prediction 2018-03-06 2024-08-08 25 True True True True prokka, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2079352 5754405 4.333333 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 2024-08-08 20 True True True True jbrowse, create_or_update, list_organism, iframe, create_account UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 1836817 4949160 4.950000 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome visualisation, Genome annotation, Read mapping 2024-01-23 2024-03-13 5 True False False True Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 967 1368 2.933333 0
Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding 2024-02-01 2024-08-01 4 True False False True Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz 0 1800 2378 2.333333 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 Multiple sequence alignment, Database search, Transcriptome assembly, Coding region prediction, De-novo assembly, Sequence alignment analysis, Phylogenetic tree generation 2022-09-08 2024-03-18 8 True False False True tab2fasta, cat1, orfipy, Add_a_column1, rbc_mafft, rapidnj, bg_diamond_view, regexColumn1, Cut1, bg_diamond_makedb, Filter1, bg_diamond, tp_split_on_column, join1, gops_intersect_1, collapse_dataset UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 974 1476 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, Primer removal, Sequence trimming, Read pre-processing 2019-07-02 2024-03-18 12 True True False True transit_gumbel, Add_a_column1, deeptools_bam_coverage, tp_easyjoin_tool, bg_find_subsequences, Cut1, Filter1, tp_sort_header_tool, bowtie_wrapper, gff_to_prot, cutadapt, __EXTRACT_DATASET__ UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 2070408 5739476 4.250000 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 visualisation, Genome annotation, Gene prediction, Coding region prediction 2018-03-06 2024-08-08 25 True True True True prokka, jbrowse UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2079352 5754405 4.333333 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 Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation 2021-03-24 2024-03-13 14 True False False True nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop UseGalaxy.eu UseGalaxy.cz 0 6851 10571 3.433333 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation 2018-06-14 2024-06-24 29 True False False True circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1 0 5938 12067 3.033333 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, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2018-02-26 2024-03-15 23 True False False True jbrowse, snippy UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 12166 20322 2.000000 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 2024-08-08 20 True True True True jbrowse, create_or_update, list_organism, iframe, create_account UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 1836817 4949160 4.950000 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome visualisation, Genome annotation, Read mapping 2024-01-23 2024-03-13 5 True False False True Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 967 1368 2.933333 0
Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding 2024-02-01 2024-08-01 4 True False False True Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz 0 1800 2378 2.333333 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 Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Sequence read processing, DNA barcoding, Sequence clustering 2017-06-22 2024-08-09 4 True False False True mothur_cluster_split, mothur_count_seqs, mothur_classify_otu, mothur_merge_files, mothur_pre_cluster, humann2_regroup_table, mothur_make_biom, mothur_make_group, mothur_screen_seqs, mothur_unique_seqs, mothur_summary_seqs, metaphlan2, humann2, krona-text, mothur_make_shared, taxonomy_krona_chart, mothur_align_seqs, humann2_renorm_table, mothur_classify_seqs, mothur_filter_seqs, metaphlan2krona UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3013 4081 2.750000 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 De-novo assembly, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Scatter plot plotting, Mapping assembly, Sequence assembly visualisation, Genome assembly, Aggregation 2019-06-25 2024-06-14 4 True False False True nanoplot, gfa_to_fa, racon, PlasFlow, miniasm, minimap2, staramr_search, bandage_image, unicycler UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1130 1752 4.016667 0
Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Statistical calculation, Aggregation 2023-05-03 2024-06-14 4 True False False True est_abundance, krakentools_kreport2krona, __UNZIP_COLLECTION__, interactive_tool_phinch, taxonomy_krona_chart, interactive_tool_pavian, kraken2, metaphlan, kraken_biom UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org.au 0 3655 4993 1.950000 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling 2022-12-05 2024-06-14 4 True False False True bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades UseGalaxy.cz, UseGalaxy.eu 0 1376 1931 2.533333 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 Visualisation, Analysis, Variant calling, DNA barcoding, Deposition 2024-06-05 2024-08-09 7 True False False True __UNZIP_COLLECTION__, phyloseq_from_dada2, interactive_tool_phyloseq, dada2_filterAndTrim, Grouping1, __SORTLIST__, dada2_learnErrors, dada2_dada, dada2_plotQualityProfile, tp_replace_in_column, dada2_removeBimeraDenovo, cat1, dada2_assignTaxonomyAddspecies, dada2_mergePairs, dada2_makeSequenceTable, collection_element_identifiers, dada2_seqCounts, tp_replace_in_line, Add_a_column1, tp_head_tool UseGalaxy.eu 0 614 840 2.066667 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 Visualisation, Sequencing quality control, Sequence composition calculation, Taxonomic classification, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Pairwise sequence alignment, Sequence assembly visualisation, Multilocus sequence typing, Cross-assembly, Genome assembly, Base-calling, Validation, Sequence assembly, Statistical calculation, Phylogenetic tree reconstruction, Sequence contamination filtering, De-novo assembly, Mapping, Box-Whisker plot plotting, Phylogenetic tree analysis, Sequence alignment analysis, Scatter plot plotting, Mapping assembly, Multiple sequence alignment, Data handling, Variant calling, Antimicrobial resistance prediction, Aggregation 2023-01-26 2024-07-26 9 True False False True __BUILD_LIST__, __FILTER_FAILED_DATASETS__, abricate, newick_display, krakentools_extract_kraken_reads, Count1, Cut1, snpSift_extractFields, kraken2, table_compute, fasta2tab, Remove beginning1, fasttree, add_line_to_file, collapse_dataset, Grep1, Grouping1, bcftools_consensus, bcftools_norm, ggplot2_heatmap, collection_column_join, clair3, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, tp_replace_in_column, CONVERTER_gz_to_uncompressed, regex1, porechop, tab2fasta, __FILTER_EMPTY_DATASETS__, taxonomy_krona_chart, tp_find_and_replace, tp_cut_tool, Paste1, flye, mlst, bedtools_getfastabed, collection_element_identifiers, bandage_image, tp_split_on_column, clustalw, regexColumn1, medaka_consensus_pipeline, samtools_coverage, krakentools_kreport2krona, barchart_gnuplot, nanoplot, param_value_from_file, compose_text_param, fastp, tp_multijoin_tool, multiqc, samtools_fastx, bamtools_split_mapped, snpSift_filter, samtools_depth, fastqc, minimap2, split_file_to_collection, Add_a_column1, tp_head_tool UseGalaxy.eu 0 1680 2521 3.016667 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 Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation 2020-11-24 2024-07-31 5 True False False True fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 0 2344 3314 2.800000 0
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification, Statistical calculation, Aggregation 2022-09-29 2024-06-14 4 True False False True fastp, taxonomy_krona_chart, fastqc, kraken2, Filter1, porechop, krakentools_kreport2krona GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1103 1743 2.816667 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 Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation 2019-11-21 2024-06-14 4 True True False True humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2066154 5729924 4.133333 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 Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation 2020-02-13 2024-06-14 4 True False False True humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 234 297 1.666667 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Sequencing quality control, Validation, Genome assembly, Sequence assembly validation, Statistical calculation, Sequence composition calculation 2023-12-05 2024-03-14 3 True False False False megahit, checkm_lineage_wf GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 1648 1997 1.483333 0
Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis 2024-03-14 2024-03-14 1 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 112 171 3.816667 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 2024-02-12 2024-03-14 3 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 119 220 2.716667 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 Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction 2019-05-13 2024-06-14 5 True False False True mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_sub_sample, mothur_classify_otu, newick_display, mothur_chimera_vsearch, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, collapse_dataset, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, mothur_summary_single, mothur_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 1744 3211 5.733333 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 Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction 2017-02-12 2024-03-14 4 True False False True mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_make_contigs, mothur_classify_otu, mothur_sub_sample, mothur_taxonomy_to_krona, mothur_chimera_vsearch, newick_display, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, mothur_make_biom, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, taxonomy_krona_chart, mothur_summary_single, mothur_cluster, mothur_seq_error, mothur_align_seqs, mothur_classify_seqs, mothur_get_groups, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 4695 7229 2.983333 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 Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction 2020-07-25 2024-07-26 30 True False False True tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__ 0 5641 8997 2.950000 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance Genome visualisation, Genome annotation, Read mapping 2024-01-23 2024-03-13 5 True False False True Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 967 1368 2.933333 0
Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction 2022-03-16 2024-07-12 12 True False False True Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 1533 2414 3.133333 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 2024-03-12 11 True False False True interactive_tool_rstudio, upload1, raxml UseGalaxy.eu UseGalaxy.fr, UseGalaxy.org (Main) 0 1308 1983 2.183333 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 Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation 2020-11-24 2024-07-31 5 True False False True fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 0 2344 3314 2.800000 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification 2020-10-29 2024-03-15 14 True False False True metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 348 504 3.800000 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification 2020-10-29 2024-03-15 14 True False False True metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 371 502 2.633333 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Label-free quantification, Filtering, Formatting, Prediction and recognition 2020-10-16 2024-03-14 20 True False False True Grep1, msconvert, peptide_shaker, search_gui, Cut1, unipept, Filter1, query_tabular, tp_replace_in_line, Remove beginning1, regex1, flashlfq, tp_replace_in_column UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 773 1343 3.800000 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 False True sqlite_to_tabular, peptide_shaker, search_gui, unipept, query_tabular UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 2256 3750 2.616667 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 Sequencing quality control, Sequence contamination filtering, Cross-assembly, Sequence composition calculation, Taxonomic classification, Expression analysis, Statistical calculation 2024-07-15 2024-07-15 1 True False False True fastp, est_abundance, fastqc, kraken2, recentrifuge, upload1 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 61 76 3.883333 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 Sequencing quality control, Genome indexing, Sequence alignment, Formatting, Sequence composition calculation, Sequence alignment analysis, Read mapping, Generation, Data handling, Variant calling, Statistical calculation 2017-02-16 2024-03-15 23 True False False True picard_MarkDuplicates, freebayes, vcf2tsv, picard_MergeSamFiles, vcffilter2, bamFilter, Cut1, fastqc, bamleftalign, bwa_mem UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 7035 13427 2.050000 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 Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction 2020-07-25 2024-07-26 30 True False False True tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__ 0 5641 8997 2.950000 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, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation 2018-02-26 2024-03-15 23 True False False True jbrowse, snippy UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 12166 20322 2.000000 0