|
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 |