|
metagenomic-raw-reads-amr-analysis/main |
WorkflowHub |
2068 |
https://workflowhub.eu/workflows/2068?version=2 |
ABRomics None, Hugo Lefeuvre |
|
2026-02-26 |
2026-05-14 |
2 |
2 |
20.0 |
table_pandas_rename_column, multiqc, groot, collection_element_identifiers, tooldistillator_summarize, tooldistillator, Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, __UNZIP_COLLECTION__, sylph_profile, argnorm, __RELABEL_FROM_FILE__, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, fastq_paired_end_interlacer, deeparg_short_reads |
Data parsing, Gene functional annotation, Validation, Taxonomic classification, Sequencing quality control, Antimicrobial resistance prediction |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
cgmlst-bacterial-genome/main |
WorkflowHub |
2055 |
https://workflowhub.eu/workflows/2055?version=2 |
ABRomics None, Clea Siguret, Hugo Lefeuvre |
|
2026-03-13 |
2026-05-14 |
2 |
2 |
3.0 |
coreprofiler_allele_calling, tooldistillator_summarize, tooldistillator |
Multilocus sequence typing, Data parsing |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
bacterial-quality-and-contamination-control-post-assembly/main |
WorkflowHub |
1882 |
https://workflowhub.eu/workflows/1882?version=3 |
ABRomics None, Pierre Marin, Clea Siguret |
|
2025-12-04 |
2026-05-13 |
3 |
3 |
14.0 |
pick_value, kraken2, tooldistillator_summarize, tooldistillator, est_abundance, quast, collapse_dataset, checkm2, recentrifuge |
Visualisation, Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Cross-assembly, Data parsing, Expression analysis, Taxonomic classification, Sequencing quality control |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE |
WorkflowHub |
155 |
https://workflowhub.eu/workflows/155?version=7 |
Peter van Heusden |
virology |
2026-03-10 |
2026-05-13 |
7 |
7 |
16.0 |
ivar_consensus, samtools_view, multiqc, __FLATTEN__, nextclade, samtools_stats, pangolin, bwa_mem, qualimap_bamqc, ivar_trim, fastp, snpeff_sars_cov_2, tp_cat, tp_sed_tool, ivar_variants |
Methylation analysis, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Variant calling, Primer removal, Sequence contamination filtering, Generation, Tree-based sequence alignment, Variant classification, Sequencing quality control |
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA |
WorkflowHub |
113 |
https://workflowhub.eu/workflows/113?version=4 |
Wolfgang Maier |
virology, covid-19, covid19.galaxyproject.org, emergen_validated |
2021-12-21 |
2026-05-14 |
4 |
4 |
11.0 |
samtools_view, multiqc, samtools_stats, bwa_mem, lofreq_viterbi, lofreq_indelqual, fastp, picard_MarkDuplicates, lofreq_call, lofreq_filter, snpeff_sars_cov_2 |
Formatting, Sequence alignment, Genome indexing, SNP detection, Validation, Read mapping, Sequence contamination filtering, Generation, Sequencing quality control |
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
generic-non-segmented-viral-variant-calling/main |
WorkflowHub |
1876 |
https://workflowhub.eu/workflows/1876?version=2 |
Peter van Heusden, Wolfgang Maier |
virology |
2025-12-05 |
2026-05-13 |
2 |
2 |
23.0 |
samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, snpEff, __FLATTEN__, samtools_stats, bwa_mem, lofreq_viterbi, calculate_numeric_param, collapse_dataset, ivar_variants, ivar_consensus, tp_find_and_replace, map_param_value, ivar_trim, fastp, tp_cat, snpSift_extractFields, pick_value, multiqc, snpEff_build_gb |
Sequence alignment, Genome indexing, Validation, Read mapping, Primer removal, Sequence contamination filtering, Generation, Sequencing quality control |
|
AGPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
influenza-isolates-consensus-and-subtyping/main |
WorkflowHub |
1260 |
https://workflowhub.eu/workflows/1260?version=3 |
Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin |
virology |
2026-02-12 |
2026-05-13 |
3 |
3 |
68.0 |
wc_gnu, samtools_view, __FILTER_FAILED_DATASETS__, tp_text_file_with_recurring_lines, qualimap_bamqc, bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample.\n__FILTER_FAILED_DATASETS__, __HARMONIZELISTS__, Show beginning1, Filter1, __FLATTEN__, collection_element_identifiers, bwa_mem, __RELABEL_FROM_FILE__, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, Paste1, bamtools_split_ref, snipit, Grep1, ivar_consensus, param_value_from_file, tp_find_and_replace, __UNZIP_COLLECTION__, tp_easyjoin_tool, fastp, tp_cat, Cut1, rbc_mafft, __FILTER_FROM_FILE__, vapor, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__, seqtk_subseq, iqtree, __DUPLICATE_FILE_TO_COLLECTION__ |
Multiple sequence alignment, Sequence alignment, Genome indexing, Sequence file editing, Phylogenetic analysis, Read mapping, Sequence analysis, Primer removal, Base position variability plotting, Sequence contamination filtering, Data retrieval, Sequence alignment analysis, Data handling, Generation, Sequencing quality control, De-novo assembly |
|
AGPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
pox-virus-amplicon/main |
WorkflowHub |
439 |
https://workflowhub.eu/workflows/439?version=4 |
Viktoria Isabel Schwarz, Wolfgang Maier |
virology, pox |
2025-10-11 |
2026-05-13 |
4 |
4 |
40.0 |
compose_text_param, samtools_view, __FILTER_FAILED_DATASETS__, qualimap_bamqc, tp_sed_tool, fasta_compute_length, samtools_merge, __FLATTEN__, collection_element_identifiers, samtools_stats, bwa_mem, __APPLY_RULES__, __ZIP_COLLECTION__, Grep1, ivar_consensus, param_value_from_file, split_file_to_collection, ivar_trim, fastp, tp_cat, Cut1, __SORTLIST__, EMBOSS: maskseq51, multiqc, datamash_ops |
Sequence alignment, Genome indexing, Validation, Read mapping, Sequence analysis, Primer removal, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Generation, Sequencing quality control |
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
allele-based-pathogen-identification/main |
WorkflowHub |
1063 |
https://workflowhub.eu/workflows/1063?version=5 |
Engy Nasr, Bérénice Batut, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
5 |
5 |
23.0 |
bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-pipeline-v5-complete/main |
WorkflowHub |
1274 |
https://workflowhub.eu/workflows/1274?version=2 |
Rand Zoabi, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
2 |
2 |
20.0 |
, fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ |
|
|
Apache-2.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-pipeline-v5-its/main |
WorkflowHub |
1273 |
https://workflowhub.eu/workflows/1273?version=2 |
Rand Zoabi, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
2 |
2 |
30.0 |
, tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ |
k-mer counting, Visualisation, Formatting, Mapping |
|
Apache-2.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-pipeline-v5-quality-control-paired-end/main |
WorkflowHub |
1272 |
https://workflowhub.eu/workflows/1272?version=2 |
Rand Zoabi, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
2 |
2 |
17.0 |
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter |
Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control |
|
Apache-2.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-pipeline-v5-quality-control-single-end/main |
WorkflowHub |
1271 |
https://workflowhub.eu/workflows/1271?version=3 |
Rand Zoabi, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
3 |
3 |
14.0 |
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter |
Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control |
|
Apache-2.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-pipeline-v5-rrna-prediction/main |
WorkflowHub |
1270 |
https://workflowhub.eu/workflows/1270?version=2 |
Rand Zoabi, Paul Zierep |
|
2025-03-26 |
2026-05-14 |
2 |
2 |
47.0 |
, bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular |
Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection |
|
Apache-2.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
mgnify-amplicon-taxonomic-summary-tables/main |
WorkflowHub |
1269 |
https://workflowhub.eu/workflows/1269?version=2 |
Rand Zoabi |
|
2025-03-26 |
2026-05-14 |
2 |
2 |
10.0 |
Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular |
|
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-discovery/main |
WorkflowHub |
1225 |
https://workflowhub.eu/workflows/1225?version=1 |
Subina Mehta |
|
2024-12-10 |
2026-05-13 |
1 |
1 |
24.0 |
Grouping1, Grep1, fasta2tab, fasta_merge_files_and_filter_unique_sequences, Filter1, ident_params, Remove beginning1, msconvert, Cut1, query_tabular, dbbuilder, fasta_cli, filter_tabular, tp_cat, search_gui, peptide_shaker, maxquant |
Visualisation, Filtering, Formatting, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering |
|
CC-BY-4.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-data-interpretation/main |
WorkflowHub |
1219 |
https://workflowhub.eu/workflows/1219?version=1 |
GalaxyP |
|
2024-11-26 |
2026-05-13 |
1 |
1 |
6.0 |
Grep1, msstatstmt, unipept |
Visualisation, Prediction and recognition |
|
CC-BY-4.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-verification/main |
WorkflowHub |
1218 |
https://workflowhub.eu/workflows/1218?version=1 |
Pratik Jagtap |
|
2024-11-26 |
2026-05-13 |
1 |
1 |
19.0 |
Grouping1, fasta_merge_files_and_filter_unique_sequences, Filter1, uniprotxml_downloader, Cut1, pepquery2, tp_cat, dbbuilder, Remove beginning1, collapse_dataset, query_tabular |
|
|
CC-BY-4.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-database-generation/main |
WorkflowHub |
1216 |
https://workflowhub.eu/workflows/1216?version=1 |
Subina Mehta |
|
2024-11-23 |
2026-05-13 |
1 |
1 |
3.0 |
metanovo, fasta_merge_files_and_filter_unique_sequences |
Expression analysis, Protein identification, Tag-based peptide identification, de Novo sequencing, Target-Decoy |
|
CC-BY-4.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-quantitation/main |
WorkflowHub |
1177 |
https://workflowhub.eu/workflows/1177?version=1 |
GalaxyP |
|
2024-10-07 |
2026-05-14 |
1 |
1 |
7.0 |
maxquant, Quantified-Proteins\nGrouping1, extract proteins\nCut1, extract peptides\nCut1, Quantified-Peptides\nGrouping1, extracting microbial Proteins\nGrep1, extracting microbial Peptides\nGrep1 |
Visualisation, Statistical calculation, Imputation, Standardisation and normalisation, Heat map generation, Protein quantification, Principal component plotting, Clustering |
|
CC-BY-4.0 |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
bacterial-genome-assembly/main |
WorkflowHub |
1043 |
https://workflowhub.eu/workflows/1043?version=12 |
Abromics None, Pierre Marin, Clea Siguret |
abromics, assembly, fastq, genomics, bacterial-genomics, paired-end, quality |
2025-12-04 |
2026-05-13 |
12 |
12 |
5.0 |
bandage_info, bandage_image, tooldistillator, tooldistillator_summarize, shovill |
Data parsing, Genome assembly, Sequence assembly visualisation |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
quality-and-contamination-control/main |
WorkflowHub |
1052 |
https://workflowhub.eu/workflows/1052?version=11 |
ABRomics None, Pierre Marin, Clea Siguret |
abromics, fastq, genomics, bacterial-genomics, paired-end, quality, taxonomy-assignment, trimming |
2025-06-19 |
2026-05-14 |
11 |
11 |
8.0 |
kraken2, tooldistillator_summarize, tooldistillator, __UNZIP_COLLECTION__, est_abundance, fastp, recentrifuge, __ZIP_COLLECTION__ |
Cross-assembly, Data parsing, Sequence contamination filtering, Expression analysis, Statistical calculation, Taxonomic classification, Sequencing quality control |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis |
WorkflowHub |
1090 |
https://workflowhub.eu/workflows/1090?version=2 |
Debjyoti Ghosh |
|
2024-11-26 |
2026-05-14 |
2 |
2 |
3.0 |
Phylogenetic tree for diversity analysis, Taxonomic analysis, Rarefaction |
|
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
gene-based-pathogen-identification/main |
WorkflowHub |
1062 |
https://workflowhub.eu/workflows/1062?version=1 |
Engy Nasr, Bérénice Batut, Paul Zierep |
|
2024-06-26 |
2026-05-13 |
1 |
1 |
15.0 |
medaka_consensus_pipeline, param_value_from_file, compose_text_param, __BUILD_LIST__, tp_find_and_replace, abricate, collection_element_identifiers, bandage_image, split_file_to_collection, flye, fasta2tab, tab2fasta |
Antimicrobial resistance prediction, Base-calling, Variant calling, Cross-assembly, Mapping assembly, Sequence assembly, Genome assembly, Sequence assembly visualisation, De-novo assembly |
|
MIT |
10.48546/workflowhub.workflow.1062.1 |
Intergalactic Workflow Commission (IWC) |
True |
False |
|
pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main |
WorkflowHub |
1060 |
https://workflowhub.eu/workflows/1060?version=1 |
Engy Nasr, Bérénice Batut, Paul Zierep |
|
2024-06-26 |
2026-05-13 |
1 |
1 |
60.0 |
Grouping1, regexColumn1, clustalw, __FILTER_FAILED_DATASETS__, fasta2tab, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, __FILTER_EMPTY_DATASETS__, bedtools_getfastabed, tp_multijoin_tool, ggplot2_heatmap, Cut1, Remove beginning1, fasttree, tp_split_on_column, collection_column_join, tp_replace_in_column, newick_display, regex1, Count1, tab2fasta |
Phylogenetic tree generation (from molecular sequences), Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Mapping, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation |
|
MIT |
10.48546/workflowhub.workflow.1060.1 |
Intergalactic Workflow Commission (IWC) |
True |
False |
|
taxonomy-profiling-and-visualization-with-krona/main |
WorkflowHub |
1059 |
https://workflowhub.eu/workflows/1059?version=1 |
Engy Nasr, Bérénice Batut, Paul Zierep |
|
2024-06-26 |
2026-05-13 |
1 |
1 |
3.0 |
kraken2, taxonomy_krona_chart, krakentools_kreport2krona |
Visualisation, Taxonomic classification, Aggregation |
|
MIT |
10.48546/workflowhub.workflow.1059.1 |
Intergalactic Workflow Commission (IWC) |
True |
False |
|
bacterial_genome_annotation/main |
WorkflowHub |
1050 |
https://workflowhub.eu/workflows/1050?version=13 |
ABRomics None, Pierre Marin, Clea Siguret |
abromics, annotation, genomics, bacterial-genomics, fasta, genome-annotation |
2025-12-06 |
2026-05-13 |
13 |
13 |
6.0 |
isescan, bakta, integron_finder, tooldistillator_summarize, tooldistillator, plasmidfinder |
Scaffolding, Multilocus sequence typing, Structural variation detection, Sequence motif recognition, Genome annotation, Data parsing, Genome assembly, Protein feature detection, Nucleic acid feature detection |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
amr_gene_detection/main |
WorkflowHub |
1049 |
https://workflowhub.eu/workflows/1049?version=9 |
ABRomics None, Pierre Marin, Clea Siguret |
abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta |
2025-12-04 |
2026-05-13 |
9 |
9 |
5.0 |
abricate, amrfinderplus, staramr_search, tooldistillator_summarize, tooldistillator |
Data parsing, Antimicrobial resistance prediction |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
dada2/main |
WorkflowHub |
790 |
https://workflowhub.eu/workflows/790?version=3 |
Matthias Bernt |
name:amplicon |
2025-03-26 |
2026-05-14 |
3 |
3 |
14.0 |
dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, dada2_makeSequenceTable, dada2_seqCounts, __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, __APPLY_RULES__, dada2_mergePairs, dada2_plotQualityProfile, dada2_dada |
DNA barcoding, Variant calling |
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
Refining Genome Annotations with Apollo (prokaryotes) |
WorkflowHub |
749 |
https://workflowhub.eu/workflows/749?version=1 |
Anthony Bretaudeau |
genome-annotation |
2024-02-14 |
2025-11-04 |
1 |
1 |
5.0 |
jbrowse, iframe, create_or_update, list_organism, create_account |
Genome visualisation |
|
CC-BY-4.0 |
10.48546/workflowhub.workflow.749.1 |
EuroScienceGateway |
True |
False |
|
TB Variant Analysis v1.0 |
WorkflowHub |
1647 |
https://workflowhub.eu/workflows/1647?version=2 |
|
gtn, galaxy, pathogen, tuberculosis |
2026-01-12 |
2026-01-12 |
2 |
2 |
15.0 |
bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 |
Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control |
|
AGPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
WorkflowHub |
2043 |
https://workflowhub.eu/workflows/2043?version=1 |
|
gtn, galaxy, sequence-analysis |
2025-12-22 |
2025-12-22 |
1 |
1 |
5.0 |
falco, kraken2, est_abundance, fastp, recentrifuge |
Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control |
|
GPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
Taxonomic Profiling and Visualization of Metagenomic Data |
WorkflowHub |
1470 |
https://workflowhub.eu/workflows/1470?version=2 |
|
gtn, galaxy, microbiome |
2025-12-22 |
2025-12-22 |
2 |
2 |
10.0 |
interactive_tool_phinch, metaphlan, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, __UNZIP_COLLECTION__, est_abundance, interactive_tool_pavian, kraken_biom |
Visualisation, Statistical calculation, Taxonomic classification, Genome annotation, Aggregation |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Checking expected species and contamination in bacterial isolate |
WorkflowHub |
1674 |
https://workflowhub.eu/workflows/1674?version=2 |
|
ecology, gtn, galaxy |
2025-12-22 |
2025-12-22 |
2 |
2 |
3.0 |
kraken2, est_abundance, recentrifuge |
Cross-assembly, Statistical calculation, Taxonomic classification, Expression analysis |
|
GPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
Metagenomic Binning |
WorkflowHub |
2028 |
https://workflowhub.eu/workflows/2028?version=1 |
|
gtn, galaxy, microgalaxy, binning, microbiome |
2025-12-08 |
2025-12-08 |
1 |
1 |
17.0 |
bowtie2, metabat2, __BUILD_LIST__, concoct_coverage_table, metabat2_jgi_summarize_bam_contig_depths, concoct_extract_fasta_bins, semibin, concoct, samtools_sort, maxbin2, binette, Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, concoct_cut_up_fasta |
Sequence assembly, Read mapping, Genome annotation, Sequence clustering, Read binning |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 - ITS |
WorkflowHub |
1856 |
https://workflowhub.eu/workflows/1856?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
30.0 |
, tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ |
k-mer counting, Visualisation, Formatting, Mapping |
|
Apache-2.0 |
|
Galaxy Training Network |
True |
False |
|
MAPseq to ampvis2 |
WorkflowHub |
1855 |
https://workflowhub.eu/workflows/1855?version=1 |
|
gtn, galaxy, microbiome |
2025-08-11 |
2025-08-11 |
1 |
1 |
9.0 |
collection_column_join, ampvis2_load, tp_awk_tool, collapse_dataset, query_tabular |
Visualisation, Analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control PE |
WorkflowHub |
1854 |
https://workflowhub.eu/workflows/1854?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
17.0 |
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter |
Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control |
|
Apache-2.0 |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 |
WorkflowHub |
1853 |
https://workflowhub.eu/workflows/1853?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
20.0 |
, fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ |
|
|
Apache-2.0 |
|
Galaxy Training Network |
True |
False |
|
MGnify amplicon summary tables |
WorkflowHub |
1851 |
https://workflowhub.eu/workflows/1851?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
10.0 |
Grouping1, collection_column_join, tp_awk_tool, filter_tabular, query_tabular |
|
|
MIT |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control SE |
WorkflowHub |
1850 |
https://workflowhub.eu/workflows/1850?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
14.0 |
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter |
Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control |
|
Apache-2.0 |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 - rRNA prediction |
WorkflowHub |
1842 |
https://workflowhub.eu/workflows/1842?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-04 |
2025-08-11 |
1 |
1 |
47.0 |
, bedtools_getfastabed, tp_awk_tool, cshl_fasta_formatter, __FILTER_FROM_FILE__, infernal_cmsearch, mapseq, collection_element_identifiers, taxonomy_krona_chart, cmsearch_deoverlap, biom_convert, gops_concat_1, __FILTER_EMPTY_DATASETS__, query_tabular |
Visualisation, Alignment, Formatting, Mapping, k-mer counting, Comparison, Nucleic acid feature detection |
|
Apache-2.0 |
|
Galaxy Training Network |
True |
False |
|
Workflow 3: Functional Information (quick) |
WorkflowHub |
1447 |
https://workflowhub.eu/workflows/1447?version=2 |
|
asaim, gtn, galaxy, metagenomics |
2025-07-14 |
2025-07-14 |
2 |
2 |
12.0 |
Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan2_humann2, Cut1, humann_renorm_table, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Building an amplicon sequence variant (ASV) table from 16S data using DADA2 |
WorkflowHub |
1395 |
https://workflowhub.eu/workflows/1395?version=2 |
|
gtn, galaxy, microbiome |
2025-07-07 |
2025-07-07 |
2 |
2 |
21.0 |
dada2_filterAndTrim, dada2_learnErrors, dada2_assignTaxonomyAddspecies, tp_replace_in_column, collection_element_identifiers, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_seqCounts, tp_replace_in_line, __UNZIP_COLLECTION__, dada2_dada, dada2_mergePairs, dada2_removeBimeraDenovo, cat1, Add_a_column1, tp_head_tool, dada2_plotQualityProfile, __SORTLIST__ |
Visualisation, DNA barcoding, Deposition, Analysis, Variant calling |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Metatranscriptomics analysis using microbiome RNA-seq data |
WorkflowHub |
1466 |
https://workflowhub.eu/workflows/1466?version=2 |
|
gtn, galaxy, microbiome |
2025-06-23 |
2025-06-23 |
2 |
2 |
33.0 |
Grouping1, metaphlan, fastqc, tp_sort_header_tool, humann, humann_unpack_pathways, graphlan, Grep1, humann_rename_table, tp_find_and_replace, combine_metaphlan_humann, Cut1, bg_sortmerna, fastq_paired_end_interlacer, humann_split_stratified_table, multiqc, cutadapt, taxonomy_krona_chart, graphlan_annotate, humann_renorm_table, humann_regroup_table, export2graphlan |
Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Phylogenetic analysis, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Species frequency estimation, Taxonomic classification, Sequence similarity search, Conversion, Aggregation |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile |
WorkflowHub |
1451 |
https://workflowhub.eu/workflows/1451?version=2 |
|
gtn, galaxy, microbiome |
2025-06-23 |
2025-06-23 |
2 |
2 |
6.0 |
graphlan, metaphlan, taxonomy_krona_chart, graphlan_annotate, Cut1, export2graphlan |
Phylogenetic tree visualisation, Visualisation, Phylogenetic inference, Phylogenetic tree editing, Taxonomic classification, Conversion |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing |
WorkflowHub |
1444 |
https://workflowhub.eu/workflows/1444?version=2 |
|
gtn, galaxy, microbiome |
2025-06-23 |
2025-06-23 |
2 |
2 |
6.0 |
multiqc, fastqc, cutadapt, bg_sortmerna, fastq_paired_end_interlacer |
Sequence trimming, Sequence composition calculation, Statistical calculation, Validation, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information |
WorkflowHub |
1456 |
https://workflowhub.eu/workflows/1456?version=2 |
|
gtn, galaxy, microbiome |
2025-06-23 |
2025-06-23 |
2 |
2 |
18.0 |
Grep1, humann_rename_table, humann, tp_find_and_replace, humann_renorm_table, tp_sort_header_tool, humann_regroup_table, humann_unpack_pathways, humann_split_stratified_table |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Assembly of metagenomic sequencing data |
WorkflowHub |
1390 |
https://workflowhub.eu/workflows/1390?version=2 |
|
gtn, galaxy, microbiome |
2025-06-16 |
2025-06-16 |
2 |
2 |
9.0 |
collection_column_join, bowtie2, megahit_contig2fastg, bandage_info, bandage_image, metaspades, quast, coverm_contig, megahit |
Visualisation, Local alignment, Sequence assembly validation, Read mapping, Genome assembly, Sequence assembly visualisation |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Taxonomic Analysis of eDNA |
WorkflowHub |
1723 |
https://workflowhub.eu/workflows/1723?version=1 |
|
ecology, gtn, galaxy |
2025-06-02 |
2025-06-02 |
1 |
1 |
8.0 |
ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp |
Sequence contamination filtering, Sequencing quality control |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
WorkflowHub |
1644 |
https://workflowhub.eu/workflows/1644?version=1 |
|
gtn, galaxy, sequence-analysis |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
falco, kraken2, est_abundance, fastp, recentrifuge |
Visualisation, Statistical calculation, Read mapping, Cross-assembly, Sequence contamination filtering, Expression analysis, Taxonomic classification, Sequencing quality control |
|
GPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
pox-virus-tiled-amplicon-ref-masking |
WorkflowHub |
1632 |
https://workflowhub.eu/workflows/1632?version=1 |
|
gtn, galaxy, variant-analysis |
2025-06-02 |
2025-06-02 |
1 |
1 |
14.0 |
Grep1, param_value_from_file, compose_text_param, EMBOSS: maskseq51, datamash_ops, Cut1, fasta_compute_length, Add_a_column1 |
Local alignment, Sequence alignment, Global alignment, Sequence alignment analysis, Sequence analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Copy Of GTN Training - Antibiotic Resistance Detection |
WorkflowHub |
1477 |
https://workflowhub.eu/workflows/1477?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
12.0 |
unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 |
Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Amplicon Tutorial |
WorkflowHub |
1476 |
https://workflowhub.eu/workflows/1476?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
17.0 |
mothur_pre_cluster, mothur_make_group, mothur_summary_seqs, mothur_count_seqs, mothur_unique_seqs, mothur_merge_files, mothur_align_seqs, mothur_filter_seqs, mothur_cluster_split, mothur_screen_seqs, mothur_classify_seqs, mothur_make_shared, krona-text, mothur_classify_otu, mothur_make_biom |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Training: 16S rRNA Analysis with Nanopore Sequencing Reads |
WorkflowHub |
1473 |
https://workflowhub.eu/workflows/1473?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
11.0 |
multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse |
Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
WGS Part In "Analyses Of Metagenomics Data - The Global Picture" |
WorkflowHub |
1472 |
https://workflowhub.eu/workflows/1472?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
7.0 |
humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, metaphlan2 |
Visualisation |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Query a metaplasmidome database to identify and annotate plasmids in metagenomes |
WorkflowHub |
1469 |
https://workflowhub.eu/workflows/1469?version=1 |
|
gtn, galaxy, metagenomics, metaplasmidome, name:microgalaxy |
2025-06-02 |
2025-06-02 |
1 |
1 |
47.0 |
Grouping1, CONVERTER_fasta_to_tabular, tp_sorted_uniq, sort1, Filter1, MQoutputfilter, tp_replace_in_column, histogram_rpy, tp_tail_tool, join1, count_gff_features, tab2fasta, Cut1, cat1, add_column_headers, Add_a_column1, ggplot2_histogram, minimap2 |
Visualisation, Pairwise sequence alignment |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Training: 16S rRNA Sequencing With Mothur: Main Tutorial |
WorkflowHub |
1465 |
https://workflowhub.eu/workflows/1465?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
38.0 |
mothur_pre_cluster, mothur_make_contigs, mothur_count_seqs, mothur_cluster, mothur_unique_seqs, mothur_venn, mothur_classify_seqs, mothur_make_shared, mothur_make_biom, mothur_summary_seqs, mothur_cluster_split, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_lineage, mothur_summary_single, mothur_remove_seqs, XY_Plot_1, mothur_remove_groups, mothur_taxonomy_to_krona, mothur_count_groups, mothur_align_seqs, mothur_filter_seqs, mothur_dist_shared, mothur_tree_shared, mothur_dist_seqs, mothur_classify_otu, mothur_heatmap_sim, mothur_rarefaction_single, mothur_sub_sample, newick_display, taxonomy_krona_chart, mothur_seq_error, mothur_get_groups |
Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' |
WorkflowHub |
1460 |
https://workflowhub.eu/workflows/1460?version=1 |
|
ecology, fungi, gtn, galaxy, lotus2, metagenomics |
2025-06-02 |
2025-06-02 |
1 |
1 |
1.0 |
lotus2 |
Sequence feature detection, DNA barcoding |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Identification of the micro-organisms in a beer using Nanopore sequencing |
WorkflowHub |
1439 |
https://workflowhub.eu/workflows/1439?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
8.0 |
kraken2, Filter1, fastqc, taxonomy_krona_chart, krakentools_kreport2krona, porechop, fastp |
Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Aggregation, Sequencing quality control |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Calculating diversity from microbiome taxonomic data |
WorkflowHub |
1431 |
https://workflowhub.eu/workflows/1431?version=1 |
|
gtn, galaxy, name:gtn |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
krakentools_alpha_diversity, krakentools_beta_diversity |
Visualisation, Aggregation |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1428 |
https://workflowhub.eu/workflows/1428?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
3.0 |
mothur_summary_seqs, mothur_classify_seqs, mothur_remove_lineage |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1422 |
https://workflowhub.eu/workflows/1422?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
5.0 |
mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1418 |
https://workflowhub.eu/workflows/1418?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
mothur_heatmap_sim, newick_display, mothur_dist_shared, mothur_venn, collapse_dataset, mothur_tree_shared |
Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1412 |
https://workflowhub.eu/workflows/1412?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
3.0 |
XY_Plot_1, mothur_rarefaction_single, mothur_summary_single |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1408 |
https://workflowhub.eu/workflows/1408?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
4.0 |
mothur_rarefaction_single, mothur_dist_seqs, mothur_make_shared, mothur_cluster |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1404 |
https://workflowhub.eu/workflows/1404?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
mothur_remove_groups, mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1400 |
https://workflowhub.eu/workflows/1400?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
9.0 |
mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
GTN Training - Antibiotic Resistance Detection |
WorkflowHub |
406 |
https://workflowhub.eu/workflows/406?version=1 |
Saskia Hiltemann, Willem de Koning |
metagenomics |
2022-11-24 |
2026-05-13 |
1 |
1 |
12.0 |
unicycler, racon, staramr_search, miniasm, nanoplot, bandage_image, PlasFlow, gfa_to_fa, minimap2 |
Aggregation, Mapping assembly, Antimicrobial resistance prediction, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly |
Microbiology |
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
3: Plant virus exploration |
WorkflowHub |
103 |
https://workflowhub.eu/workflows/103?version=1 |
|
de_novo, virology, exploration |
2021-02-04 |
2026-05-13 |
1 |
1 |
2.0 |
fastp, shovill |
Genome assembly, Sequence contamination filtering, Sequencing quality control |
|
Apache-2.0 |
|
Integrated and Urban Plant Pathology Laboratory |
True |
False |
|
2: Plant virus confirmation |
WorkflowHub |
102 |
https://workflowhub.eu/workflows/102?version=1 |
|
assembly, virology, blast, mapping, reads_selection |
2021-02-04 |
2026-05-13 |
1 |
1 |
7.0 |
fasta_merge_files_and_filter_unique_sequences, ncbi_blastn_wrapper, samtools_stats, picard_SamToFastq, shovill, ngsutils_bam_filter, minimap2 |
Read pre-processing, Sequence contamination filtering, Formatting, Pairwise sequence alignment, Genome assembly, Sequencing quality control, Variant calling |
|
Apache-2.0 |
|
Integrated and Urban Plant Pathology Laboratory |
True |
False |
|
1: Plant virus detection with kraken2 (SE) |
WorkflowHub |
124 |
https://workflowhub.eu/workflows/124?version=1 |
|
virology, kraken |
2021-06-17 |
2026-05-13 |
1 |
1 |
3.0 |
kraken2, Kraken2Tax, taxonomy_krona_chart |
Visualisation, Taxonomic classification |
|
Apache-2.0 |
|
Integrated and Urban Plant Pathology Laboratory |
True |
False |
|
1: Plant virus detection with kraken2 (PE) |
WorkflowHub |
101 |
https://workflowhub.eu/workflows/101?version=1 |
|
virology, kraken |
2021-02-04 |
2026-05-13 |
1 |
1 |
3.0 |
kraken2, Kraken2Tax, taxonomy_krona_chart |
Visualisation, Taxonomic classification |
|
Apache-2.0 |
|
Integrated and Urban Plant Pathology Laboratory |
True |
False |
|
Taxonomy Assignment with QIIME2 |
WorkflowHub |
2098 |
https://workflowhub.eu/workflows/2098?version=1 |
Tristan Reynolds, Amy Loughman |
amplicon, microbiome, taxonomic-classification |
2026-03-02 |
2026-05-13 |
1 |
1 |
19.0 |
qiime2__feature_classifier__classify_sklearn, qiime2__feature_table__summarize, qiime2_core__tools__import, qiime2__taxa__barplot, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_table__tabulate_seqs, qiime2__feature_classifier__extract_reads, csv_to_tabular, tp_easyjoin_tool, Remove beginning1, biom_convert, qiime_extract_viz, qiime2_core__tools__export, tabular_to_csv |
Visualisation, Formatting, Demultiplexing, Taxonomic classification |
Taxonomy |
CC-BY-4.0 |
10.48546/workflowhub.workflow.2098.1 |
Melbourne Bioinformatics, Galaxy Australia |
True |
False |
|
Taxonomy classification using Kraken2 and Bracken |
WorkflowHub |
1199 |
https://workflowhub.eu/workflows/1199?version=2 |
Valentine Murigneux, Mike Thang |
gucfg2galaxy, metagenomics, name:collection, shotgun |
2024-12-10 |
2024-12-10 |
2 |
2 |
29.0 |
collection_column_join, krakentools_beta_diversity, Prepare alpha diversity summary file\nPaste1, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, kraken2, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, taxonomy_krona_chart, collection_element_identifiers, krakentools_kreport2krona, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1, est_abundance, __RELABEL_FROM_FILE__, add_line_to_file, regex1, krakentools_alpha_diversity, cat_multiple, Extract column name and fraction_total_reads from Bracken report\nCut1, krakentools_combine_kreports |
Visualisation, Statistical calculation, Taxonomic classification, Aggregation |
Metagenomics, Taxonomy |
CC-BY-4.0 |
10.48546/workflowhub.workflow.1199.2 |
QCIF Bioinformatics |
True |
False |
|
Analyses of shotgun metagenomics data with MetaPhlAn2 |
WorkflowHub |
624 |
https://workflowhub.eu/workflows/624?version=1 |
Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut |
gucfg2galaxy, metagenomics, shotgun |
2023-10-26 |
2026-05-13 |
1 |
1 |
17.0 |
, humann2, taxonomy_krona_chart, metaphlan2krona, humann2_renorm_table, humann2_regroup_table, Cut1, merge_metaphlan_tables, metaphlan2 |
Visualisation, Taxonomic classification |
Metagenomic sequencing, Metagenomics |
CC-BY-4.0 |
10.48546/workflowhub.workflow.624.1 |
QCIF Bioinformatics |
True |
False |
|
Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur] |
WorkflowHub |
653 |
https://workflowhub.eu/workflows/653?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
4.0 |
mothur_dist_shared, mothur_tree_shared, mothur_heatmap_sim, newick_display |
Visualisation, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree generation, DNA barcoding, Phylogenetic tree analysis, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur] |
WorkflowHub |
652 |
https://workflowhub.eu/workflows/652?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
3.0 |
XY_Plot_1, mothur_rarefaction_single, mothur_summary_single |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur] |
WorkflowHub |
651 |
https://workflowhub.eu/workflows/651?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
5.0 |
mothur_sub_sample, mothur_count_groups, mothur_cluster_split, mothur_make_shared, mothur_classify_otu |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
650 |
https://workflowhub.eu/workflows/650?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
2.0 |
mothur_classify_seqs, mothur_remove_lineage |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur] |
WorkflowHub |
648 |
https://workflowhub.eu/workflows/648?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
5.0 |
mothur_summary_seqs, mothur_count_seqs, mothur_screen_seqs, mothur_unique_seqs |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur] |
WorkflowHub |
649 |
https://workflowhub.eu/workflows/649?version=1 |
Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi |
metagenomics |
2023-11-09 |
2026-05-13 |
1 |
1 |
9.0 |
mothur_pre_cluster, mothur_summary_seqs, mothur_unique_seqs, mothur_filter_seqs, mothur_chimera_vsearch, mothur_screen_seqs, mothur_remove_seqs |
Visualisation, Sequence clustering, DNA barcoding, Taxonomic classification, Sequence read processing, Sequencing quality control, Phylogenetic analysis |
|
CC-BY-4.0 |
|
QCIF Bioinformatics |
True |
False |
|
TB Variant Analysis v1.0 |
WorkflowHub |
1035 |
https://workflowhub.eu/workflows/1035?version=1 |
Peter van Heusden |
pathogen, tuberculosis |
2024-06-07 |
2026-05-13 |
1 |
1 |
15.0 |
bcftools_consensus, tp_awk_tool, tb_profiler_profile, kraken2, __FLATTEN__, multiqc, mosdepth, snippy, qualimap_bamqc, tb_variant_filter, tbvcfreport, fastp, tp_sed_tool, EMBOSS: seqret84 |
Phylogenetic tree visualisation, Sequence alignment, Validation, Antimicrobial resistance prediction, Phylogenetic tree generation, Variant calling, Sequence analysis, Local alignment, Sequence contamination filtering, Global alignment, Sequence alignment analysis, Taxonomic classification, Sequencing quality control |
Genetic variation, Infectious disease, Microbiology, Public health and epidemiology, Sequence assembly |
AGPL-3.0-or-later |
|
SANBI Pathogen Bioinformatics |
True |
False |
|
Workflow 3: AMR - SeqSero2/SISTR |
WorkflowHub |
407 |
https://workflowhub.eu/workflows/407?version=1 |
|
bioinformatics, antimicrobial resistance |
2022-11-24 |
2026-05-13 |
1 |
1 |
14.0 |
kma_map, hamronize_summarize, seqsero2, bbtools_bbduk, __UNZIP_COLLECTION__, srst2, shovill, mob_recon, hamronize_tool, sistr_cmd, bbtools_tadpole |
Visualisation, Multilocus sequence typing, Sequence alignment, Genome indexing, Read mapping, Sequence contamination filtering, Clustering, Genome alignment, Parsing, Data handling, Genome assembly, RNA-Seq analysis, Sequence trimming, Antimicrobial resistance prediction, Read binning, Sequence analysis |
|
GPL-3.0 |
|
Seq4AMR |
True |
False |
|
Workflow 2: Sciensano |
WorkflowHub |
644 |
https://workflowhub.eu/workflows/644?version=1 |
|
|
2023-11-07 |
2026-05-13 |
1 |
1 |
1.0 |
pipeline_stec_1.0 |
|
|
CC-BY-4.0 |
|
Seq4AMR |
True |
False |
|
Workflow 4: Staramr |
WorkflowHub |
470 |
https://workflowhub.eu/workflows/470?version=1 |
|
10.3390/microorganisms10020292, amr, amr-detection, bioinformatics, antimicrobial resistance |
2023-05-11 |
2026-05-13 |
1 |
1 |
10.0 |
hamronize_summarize, tp_find_and_replace, abricate, staramr_search, collapse_dataset, shovill, hamronize_tool |
Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction |
|
GPL-3.0 |
|
Seq4AMR |
True |
False |
|
Workflow 1: AbritAMR |
WorkflowHub |
634 |
https://workflowhub.eu/workflows/634?version=1 |
|
|
2023-10-31 |
2026-05-13 |
1 |
1 |
1.0 |
abritamr |
Antimicrobial resistance prediction |
|
CC-BY-4.0 |
|
Seq4AMR |
True |
False |
|
AMR-Pathfinder |
WorkflowHub |
1189 |
https://workflowhub.eu/workflows/1189?version=2 |
Helena Rasche, Dennis Dollée, Birgit Rijvers |
amr, amr-detection, benchamrking |
2024-11-14 |
2026-05-13 |
2 |
2 |
36.0 |
, hamronize_summarize, tp_text_file_with_recurring_lines, cat1, hamronize_tool, abricate, addValue, __APPLY_RULES__, __MERGE_COLLECTION__, collapse_dataset, shovill, Grep1, cast, tp_find_and_replace, Cut1, tp_split_on_column, datamash_ops, staramr_search, cat_multi_datasets |
Parsing, Data handling, Genome assembly, Antimicrobial resistance prediction |
|
MIT |
|
Seq4AMR, ErasmusMC Clinical Bioinformatics |
True |
False |
|
Copy of Metaproteomics_GTN shared by user engy.nasr |
https://usegalaxy.eu |
6ca1b4fe047a03d2 |
https://usegalaxy.eu/published/workflow?id=6ca1b4fe047a03d2 |
|
proteomics, name:microgalaxy |
2026-04-27 |
2026-04-27 |
1 |
1 |
|
search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept |
Visualisation, Prediction and recognition |
|
|
|
|
True |
False |
|
Training: 16S rRNA Analysis with Nanopore Sequencing Reads |
https://usegalaxy.eu |
2a093e63ebf6876b |
https://usegalaxy.eu/published/workflow?id=2a093e63ebf6876b |
|
metagenomics, name:microgalaxy |
2025-12-01 |
2026-03-16 |
2 |
2 |
|
multiqc, kraken2, fastqc, taxonomy_krona_chart, porechop, tp_replace_in_line, fastp, Remove beginning1, datamash_reverse |
Visualisation, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Taxonomic classification, Sequencing quality control |
|
|
|
|
True |
False |
|
MetaG_extended |
https://usegalaxy.eu |
8c91345ed468e22d |
https://usegalaxy.eu/published/workflow?id=8c91345ed468e22d |
|
name:microgalaxy |
2025-10-01 |
2026-02-04 |
0 |
0 |
|
fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, cat_bins, tp_cat, trim_galore, interproscan, sort1 |
Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation |
|
|
|
|
True |
False |
|
Metagenomic Taxonomy Analysis |
https://usegalaxy.eu |
7491883694fff308 |
https://usegalaxy.eu/published/workflow?id=7491883694fff308 |
Bérénice Batut, Géraldine Piot, Mina Hojat Ansari |
name:metagenomics, microbiome, diversity, name:microgalaxy |
2025-11-28 |
2025-12-17 |
3 |
3 |
|
metaphlan, kraken2, collection_element_identifiers, taxonomy_krona_chart, metaphlan2krona, krakentools_kreport2krona, taxpasta, est_abundance, sylph_profile, add_line_to_file, datamash_transpose, Remove beginning1, cat1 |
Visualisation, Formatting, Statistical calculation, Taxonomic classification, Conversion, Aggregation, Standardisation and normalisation |
|
MIT |
|
|
True |
False |
|
Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT |
https://usegalaxy.eu |
7371b6918e895e0c |
https://usegalaxy.eu/published/workflow?id=7371b6918e895e0c |
Bérénice Batut |
microbiome, name:microgalaxy |
2025-12-01 |
2025-12-08 |
16 |
16 |
|
multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 |
Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
pAllori Amplicon 16S Pre-Processing and Taxonomy Classification |
https://usegalaxy.eu |
466bdd8ba7b67264 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 |
Engy Nasr, Paul Zierep |
name:microgalaxy, name:16s, name:metagenomics, name:pallori |
2023-06-30 |
2025-11-18 |
193 |
193 |
|
compose_text_param, ampvis2_heatmap, fastqc, bg_column_arrange_by_header, ampvis2_subset_samples, datamash_transpose, unzip, biom_convert, maaslin2, volcanoplot, __FLATTEN__, calculate_numeric_param, mmuphin, phyloseq_tax_glom, ampvis2_load, param_value_from_file, tp_awk_tool, tp_cut_tool, tp_easyjoin_tool, Remove beginning1, multiqc, ampvis2_ordinate, phyloseq_from_biom, phyloseq_add_rank_names, ampvis2_export_otu, regex1, lotus2, decontam |
Visualisation, Sequence feature detection, Sequence composition calculation, Filtering, Formatting, Statistical calculation, Deposition, Validation, Analysis, Standardisation and normalisation, Classification, DNA barcoding, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Metagenomic Taxonomy and Functional Analysis |
https://usegalaxy.eu |
cb2df493f5e334f7 |
https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 |
Bérénice Batut, Géraldine Piot |
name:metagenomics, microbiome, diversity, name:microgalaxy |
2024-12-20 |
2025-11-13 |
18 |
18 |
|
metaphlan, tp_text_file_with_recurring_lines, est_abundance, datamash_transpose, cat1, tp_sed_tool, sort1, humann, kraken2, collection_element_identifiers, krakentools_kreport2krona, csv_to_tabular, collapse_dataset, humann_unpack_pathways, humann_rename_table, tp_awk_tool, tp_replace_in_line, __UNZIP_COLLECTION__, add_line_to_file, tp_easyjoin_tool, Remove beginning1, krakentools_alpha_diversity, fastq_paired_end_interlacer, collection_column_join, taxonomy_krona_chart, taxpasta, sylph_profile, humann_renorm_table, humann_regroup_table |
Visualisation, Formatting, Statistical calculation, Standardisation and normalisation, Species frequency estimation, Taxonomic classification, Conversion, Aggregation, Phylogenetic analysis |
|
MIT |
|
|
True |
False |
|
pAllori Blood RNA |
https://usegalaxy.eu |
ca9d3233b0912765 |
https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 |
Engy Nasr, Paul Zierep |
name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics |
2023-07-02 |
2025-06-26 |
48 |
48 |
|
collection_column_join, multiqc, fastqc, __FILTER_FAILED_DATASETS__, featurecounts, umi_tools_dedup, rna_star, umi_tools_extract |
Read summarisation, Sequence composition calculation, RNA-Seq quantification, Statistical calculation, Sequence alignment, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
MetaG: Preparation, Building and Annotation of Metagenomics Assembled Genomes |
https://usegalaxy.eu |
667bac8d7453e5f1 |
https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1 |
Valerie C. Schiml, Magnus Ø. Arntzen, Bérénice Batut |
name:microgalaxy, name:microbiome, name:mags |
2024-09-30 |
2024-12-21 |
14 |
14 |
|
fasplit, tp_awk_tool, tp_grep_tool, fastqc, checkm_lineage_wf, hmmer_hmmscan, coverm_genome, quast, coverm_contig, fraggenescan, maxbin2, tp_cat, cat_bins, kofamscan, trim_galore, interproscan, sort1 |
Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Gene functional annotation, Validation, Sequence database search, Format validation, Primer removal, Coding region prediction, Local alignment, Sequence assembly, Database search, Sequence profile generation, Sequencing quality control, Protein feature detection, Sequence trimming, Multiple sequence alignment, Sequence assembly validation, Sequence motif recognition, Sequence generation, Sequence analysis, Read pre-processing, Data retrieval, Gene prediction, Taxonomic classification, Conversion, Probabilistic sequence generation |
|
MIT |
|
|
True |
False |
|
ASaiM-MT: Metatranscriptomics Analysis of Microbes |
https://usegalaxy.eu |
096b75501c8e0888 |
https://usegalaxy.eu/published/workflow?id=096b75501c8e0888 |
Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap |
asaim, metatranscriptomics, rna-seq, microbiome, name:microgalaxy |
2024-12-20 |
2024-12-20 |
3 |
3 |
|
Grouping1, group_humann2_uniref_abundances_to_go, fastqc, humann2_renorm_table, humann2_unpack_pathways, tp_sort_header_tool, humann2_genefamilies_genus_level, humann2, metaphlan2krona, Grep1, format_metaphlan2_output, graphlan, bg_sortmerna, fastq_paired_end_interlacer, multiqc, combine_metaphlan2_humann2, cutadapt, taxonomy_krona_chart, graphlan_annotate, export2graphlan, metaphlan2 |
Sequence comparison, Phylogenetic tree visualisation, Visualisation, Sequence composition calculation, Formatting, Statistical calculation, Phylogenetic inference, Validation, Primer removal, Sequence alignment analysis, Sequencing quality control, Sequence trimming, Phylogenetic tree editing, Read pre-processing, Taxonomic classification, Sequence similarity search, Conversion |
|
MIT |
|
|
True |
False |
|
MetaT: Metatranscriptomics data analysis |
https://usegalaxy.eu |
fd90652d475ed739 |
https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 |
Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin |
name:microgalaxy, metatranscriptomics, microbiome |
2024-11-21 |
2024-12-20 |
6 |
6 |
|
collection_column_join, kallisto_quant, fastqc, __UNZIP_COLLECTION__, trim_galore, bg_sortmerna |
Sequence trimming, Sequence composition calculation, Statistical calculation, Gene expression profiling, Primer removal, Read pre-processing, Sequence similarity search, Sequence alignment analysis, Sequence comparison, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Halophiles workup of Comparative gene analysis |
https://usegalaxy.eu |
a2c46deea34d9d80 |
https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 |
Anton Nekrutenko |
genome-annotation, name:microgalaxy |
2024-12-03 |
2024-12-05 |
2 |
2 |
|
tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 |
Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation |
|
|
|
|
True |
False |
|
Metaproteomics workflow |
https://usegalaxy.eu |
cefc49c13ff73231 |
https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 |
Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta |
name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy |
2024-11-21 |
2024-11-21 |
40 |
40 |
|
search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept |
Visualisation, Prediction and recognition |
|
MIT |
|
|
True |
False |
|
Feature-Count Table Normalization |
https://usegalaxy.eu |
6239178d7cc4ac68 |
https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 |
Johannes Effenberger |
name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle |
2024-11-21 |
2024-11-21 |
5 |
5 |
|
Grep1, __BUILD_LIST__, map_param_value, __EXTRACT_DATASET__, __FILTER_EMPTY_DATASETS__ |
|
|
MIT |
|
|
True |
False |
|
metaQuantome_datacreation_workflow |
https://usegalaxy.eu |
cd675ab32d3e7833 |
https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 |
Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane |
proteomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
1 |
1 |
|
tp_replace_in_column, flashlfq, Filter1, msconvert, tp_replace_in_line, Cut1, regex1, Remove beginning1, search_gui, peptide_shaker, query_tabular, unipept |
Visualisation, Label-free quantification, Prediction and recognition, Filtering, Formatting |
|
MIT |
|
|
True |
False |
|
metaquantome-function-worklow |
https://usegalaxy.eu |
e5a89ef7b5f1c1d9 |
https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 |
Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar |
proteomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
3 |
3 |
|
metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_filter, metaquantome_viz, metaquantome_expand |
Visualisation, Statistical inference, Quantification, Heat map generation, Query and retrieval, Indexing, Differential protein expression analysis, Principal component visualisation, Filtering, Functional clustering |
|
MIT |
|
|
True |
False |
|
Cloud Aerosol MT-MG Contamination Filtering |
https://usegalaxy.eu |
c09159d7aad0f264 |
https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 |
Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato |
metagenomics, metatranscriptomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
2 |
2 |
|
bowtie2, kraken2, fastq_to_tabular, filter_tabular, recentrifuge, seq_filter_by_id |
Cross-assembly, Taxonomic classification, Read mapping, Expression analysis |
|
MIT |
|
|
True |
False |
|
Cloud-Aerosole MT-MG Functional Profiling |
https://usegalaxy.eu |
63478edcea3f449a |
https://usegalaxy.eu/published/workflow?id=63478edcea3f449a |
Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato |
metagenomics, metatranscriptomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
4 |
4 |
|
featurecounts, bowtie2, multiqc |
Read summarisation, RNA-Seq quantification, Validation, Read mapping, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Cloud-Aerosole MT-MG Pre-Processing |
https://usegalaxy.eu |
1ef76b7b86e15792 |
https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 |
Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato |
metagenomics, metatranscriptomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
6 |
6 |
|
trimmomatic, fastqc, multiqc |
Sequence composition calculation, Statistical calculation, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Mgnify ML |
https://usegalaxy.eu |
011f701c5a55bfdf |
https://usegalaxy.eu/published/workflow?id=011f701c5a55bfdf |
|
name:microgalaxy |
2023-10-10 |
2024-03-15 |
128 |
128 |
|
interactive_tool_jupyter_notebook, __BUILD_LIST__ |
|
|
|
|
|
True |
False |
|
Ecoli Comparison |
https://usegalaxy.eu |
0e492839192d26e0 |
https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 |
|
assembly, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
mergeCols1, bedtools_complementbed, tp_sort_header_tool, tp_sed_tool, cat1, bedtools_sortbed, fasta_compute_length, Filter1, addValue, join1, collapse_dataset, bedtools_intersectbed, random_lines1, Grep1, tp_cat, Cut1, fasta_filter_by_length, tp_grep_tool, datamash_ops, lastz_wrapper_2 |
Read mapping, Sequence alignment, Mapping |
|
|
|
|
True |
False |
|
Comparative gene analysis |
https://usegalaxy.eu |
86900be4282d4b1d |
https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d |
Anton Nekrutenko |
vgp, genome-annotation, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
tp_split_on_column, regexColumn1, rbc_mafft, bg_diamond_view, Filter1, bg_diamond, join1, tab2fasta, collapse_dataset, Cut1, cat1, rapidnj, Add_a_column1, gops_intersect_1 |
Sequence alignment analysis, Multiple sequence alignment, Phylogenetic tree generation |
|
|
|
|
True |
False |
|
Apollo Load Test |
https://usegalaxy.eu |
3c233cc56d4df8b0 |
https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0 |
|
genome-annotation, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
jbrowse, iframe, create_or_update, list_organism, create_account |
Genome visualisation |
|
|
|
|
True |
False |
|
Flye-AMR workflow EMC/WMDI - v3.5 (imported from URL) |
https://usegalaxy.eu |
152223c8aed27357 |
https://usegalaxy.eu/published/workflow?id=152223c8aed27357 |
|
wmdi, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
jbrowse, bg_column_arrange_by_header, gff2bed1, tp_text_file_with_recurring_lines, circos_gc_skew, trimmomatic, fasta2tab, fasta_compute_length, Add_a_column1, circos_interval_to_tile, tp_sort_header_tool, minimap2, Filter1, bandage_image, nanoplot, join1, PlasFlow, circos, tp_head_tool, deeptools_bam_coverage, Grep1, tp_cut_tool, tp_easyjoin_tool, tp_cat, regex_replace, Cut1, tp_split_on_column, medaka_consensus_pipeline, circos_wiggle_to_scatter, ncbi_blastn_wrapper, staramr_search, prokka, regex1, flye, tbl2gff3, tab2fasta |
Genome assembly, Sequence visualisation, Gene prediction, Genome annotation, Sequence analysis, Variant calling, Base-calling, Antimicrobial resistance prediction, Coding region prediction, Cross-assembly, Mapping assembly, Sequence assembly, Box-Whisker plot plotting, Genome visualisation, Pairwise sequence alignment, Sequence assembly visualisation, Scatter plot plotting, De-novo assembly |
|
|
|
|
True |
False |
|
From VCFs to SNP distance matrix |
https://usegalaxy.eu |
6d333ed886aab471 |
https://usegalaxy.eu/published/workflow?id=6d333ed886aab471 |
|
evolution, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
bcftools_consensus, snp_sites, tb_variant_filter, tp_cat, snp_dists |
|
|
|
|
|
True |
False |
|
From Fastqs to VCFs and BAMs |
https://usegalaxy.eu |
3a8fde248a4d0383 |
https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383 |
|
evolution, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
trimmomatic, tb_variant_filter, __MERGE_COLLECTION__, snippy |
Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation |
|
|
|
|
True |
False |
|
From BAMs to drug resistance prediction with TB-profiler |
https://usegalaxy.eu |
d0d6dae0d1eecc21 |
https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21 |
|
evolution, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
samtools_view, tb_profiler_profile, tp_grep_tool, tp_replace_in_line, __MERGE_COLLECTION__, tp_cat, addName, tp_sed_tool |
Antimicrobial resistance prediction |
|
|
|
|
True |
False |
|
Compute Allel Frequency Table from paired reads |
https://usegalaxy.eu |
21a39ac4c1becb31 |
https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31 |
|
name:microgalaxy, hpylori |
2023-12-13 |
2023-12-13 |
2 |
2 |
|
bowtie2, bcftools_norm, tp_awk_tool, snpSift_filter, vcf2tsv, freebayes, bcftools_view |
Read mapping, Statistical calculation, Variant calling |
|
|
|
|
True |
False |
|
Reference genome choice (indels, coverage, depth) for short reads |
https://usegalaxy.eu |
61fe08fb3d5e83f8 |
https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8 |
|
name:microgalaxy, hpylori |
2023-10-27 |
2023-12-13 |
13 |
13 |
|
bowtie2, samtools_coverage, bcftools_norm, vcf2tsv, collection_element_identifiers, freebayes, tp_cat, collapse_dataset, samtools_depth |
Read mapping, Statistical calculation, Variant calling |
|
|
|
|
True |
False |
|
Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT |
https://usegalaxy.fr |
f0776f7a890b523a |
https://usegalaxy.fr/published/workflow?id=f0776f7a890b523a |
Bérénice Batut |
microbiome, name:microgalaxy |
2025-12-08 |
2025-12-08 |
1 |
1 |
|
multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 |
Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT |
https://usegalaxy.org |
a8aee61c2cbaf6ea |
https://usegalaxy.org/published/workflow?id=a8aee61c2cbaf6ea |
Bérénice Batut |
microbiome, name:microgalaxy |
2025-12-08 |
2025-12-08 |
1 |
1 |
|
multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 |
Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 (release v0.1) |
https://usegalaxy.org |
8e863bbef37cc36b |
https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, metagenomics, amplicon, name:microgalaxy |
2025-02-06 |
2025-04-25 |
1 |
1 |
|
fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ |
|
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - ITS (release v0.1) |
https://usegalaxy.org |
45f959d5bf505b15 |
https://usegalaxy.org/published/workflow?id=45f959d5bf505b15 |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-02-06 |
2025-04-25 |
1 |
1 |
|
tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ |
k-mer counting, Visualisation, Formatting, Mapping |
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.1) |
https://usegalaxy.org |
a71fcbc60caae8b6 |
https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6 |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-02-06 |
2025-04-25 |
1 |
1 |
|
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter |
Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control |
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.1) |
https://usegalaxy.org |
5f878c4cc3bff68c |
https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c |
MGnify - EMBL, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-02-06 |
2025-04-25 |
1 |
1 |
|
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter |
Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control |
|
Apache-2.0 |
|
|
True |
False |
|
Allele-based Pathogen Identification (release v0.1.3) |
https://usegalaxy.org |
3e703abaeb870f6f |
https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f |
Engy Nasr, Bérénice Batut, Paul Zierep |
name:collection, name:microgalaxy, name:pathogfair, name:iwc |
2025-03-06 |
2025-04-25 |
1 |
1 |
|
bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.2) |
https://usegalaxy.org |
afb67b4b9952f57d |
https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d |
MGnify - EMBL, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-03-06 |
2025-04-25 |
1 |
1 |
|
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter |
Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control |
|
Apache-2.0 |
|
|
True |
False |
|
Allele-based Pathogen Identification (release v0.1.4) |
https://usegalaxy.org |
cb810cdaa4915f4b |
https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b |
Engy Nasr, Bérénice Batut, Paul Zierep |
name:collection, name:microgalaxy, name:pathogfair, name:iwc |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 (release v0.2) |
https://usegalaxy.org |
77de7101effbff3d |
https://usegalaxy.org/published/workflow?id=77de7101effbff3d |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, metagenomics, amplicon, name:microgalaxy |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
fastq_dl, CONVERTER_uncompressed_to_gz, tp_awk_tool, CONVERTER_gz_to_uncompressed, __MERGE_COLLECTION__ |
|
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - ITS (release v0.2) |
https://usegalaxy.org |
8151be18aab3a3c6 |
https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6 |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
tp_awk_tool, __FILTER_FROM_FILE__, bedtools_maskfastabed, mapseq, collection_element_identifiers, taxonomy_krona_chart, biom_convert, __FILTER_EMPTY_DATASETS__ |
k-mer counting, Visualisation, Formatting, Mapping |
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control PE (release v0.2) |
https://usegalaxy.org |
20b7ae4b517a80fd |
https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, __UNZIP_COLLECTION__, prinseq, mgnify_seqprep, fastp, trimmomatic, fastq_filter |
Sequence trimming, Sequence composition calculation, Nucleic acid design, Statistical calculation, Validation, Read pre-processing, Sequence contamination filtering, Sequencing quality control |
|
Apache-2.0 |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control SE (release v0.3) |
https://usegalaxy.org |
46f184a0e95f3c1c |
https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c |
MGnify - EMBL, Rand Zoabi, Paul Zierep |
mgnify_amplicon, amplicon, metagenomics, name:microgalaxy |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
cshl_fasta_formatter, tp_find_and_replace, fastq_to_fasta_python, multiqc, fastqc, prinseq, trimmomatic, fastq_filter |
Sequence trimming, Read pre-processing, Sequence composition calculation, Sequence contamination filtering, Statistical calculation, Validation, Sequencing quality control |
|
Apache-2.0 |
|
|
True |
False |
|
Nanopore Preprocessing (release v0.1) |
https://usegalaxy.org |
a8b9252fad5fe06a |
https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a |
Bérénice Batut, Engy Nasr, Paul Zierep |
name:collection, name:microgalaxy, name:pathogfair, name:nanopore, name:iwc |
2025-03-20 |
2025-04-25 |
1 |
1 |
|
collection_column_join, Grep1, samtools_fastx, regexColumn1, multiqc, kraken2, fastqc, bamtools_split_mapped, nanoplot, porechop, __FILTER_FAILED_DATASETS__, krakentools_extract_kraken_reads, fastp, collapse_dataset, Cut1, Add_a_column1, minimap2 |
Visualisation, Sequence composition calculation, Statistical calculation, Validation, Sequence contamination filtering, Box-Whisker plot plotting, Sequence alignment analysis, Taxonomic classification, Data handling, Pairwise sequence alignment, Aggregation, Scatter plot plotting, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Quality control of bins generated by MetaBAT2, MaxBin2, SemiBin, and CONCOCT |
https://usegalaxy.org.au |
f05ed1e5c5dfffa9 |
https://usegalaxy.org.au/published/workflow?id=f05ed1e5c5dfffa9 |
Bérénice Batut |
microbiome, name:microgalaxy |
2025-12-08 |
2025-12-08 |
1 |
1 |
|
multiqc, __FLATTEN__, collection_element_identifiers, __RELABEL_FROM_FILE__, __MERGE_COLLECTION__, regex1, checkm2 |
Sequence composition calculation, Sequence assembly validation, Statistical calculation, Validation, Sequencing quality control |
|
MIT |
|
|
True |
False |
|
Allele-based Pathogen Identification (release v0.1.3) |
https://usegalaxy.org.au |
0e11619979c2830c |
https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c |
Engy Nasr, Bérénice Batut, Paul Zierep |
name:collection, name:microgalaxy, name:pathogfair, name:iwc |
2025-03-06 |
2025-04-25 |
1 |
1 |
|
bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |
|
Allele-based Pathogen Identification (release v0.1.4) |
https://usegalaxy.org.au |
76a0a3af8de11622 |
https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622 |
Engy Nasr, Bérénice Batut, Paul Zierep |
name:collection, name:microgalaxy, name:pathogfair, name:iwc |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
bcftools_consensus, Paste1, samtools_coverage, regexColumn1, bcftools_norm, CONVERTER_gz_to_uncompressed, snpSift_filter, tp_cut_tool, Cut1, snpSift_extractFields, clair3, collapse_dataset, Remove beginning1, table_compute, tp_head_tool, Count1, samtools_depth, minimap2 |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |