|
metagenomic-raw-reads-amr-analysis/main |
WorkflowHub |
2068 |
https://workflowhub.eu/workflows/2068?version=2 |
ABRomics None, Hugo Lefeuvre |
|
2026-02-26 |
2026-02-27 |
2 |
2 |
20.0 |
Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__, __FILTER_FAILED_DATASETS__, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, fastq_paired_end_interlacer, tooldistillator, deeparg_short_reads, multiqc, argnorm, __UNZIP_COLLECTION__, sylph_profile, __RELABEL_FROM_FILE__, tooldistillator_summarize, groot, tp_text_file_with_recurring_lines, table_pandas_rename_column, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, collection_element_identifiers |
Gene functional annotation, Sequencing quality control, Validation, Data parsing, Antimicrobial resistance prediction, Taxonomic classification |
|
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 |
2026-03-13 |
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 |
2025-12-04 |
3 |
3 |
14.0 |
kraken2, recentrifuge, tooldistillator, tooldistillator_summarize, est_abundance, checkm2, pick_value, collapse_dataset, quast |
Visualisation, Validation, Taxonomic classification, Expression analysis, Statistical calculation, Sequencing quality control, Sequence composition calculation, Data parsing, Sequence assembly validation, Cross-assembly |
|
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 |
2026-03-10 |
7 |
7 |
16.0 |
qualimap_bamqc, ivar_trim, ivar_consensus, snpeff_sars_cov_2, pangolin, tp_sed_tool, ivar_variants, samtools_stats, __FLATTEN__, multiqc, tp_cat, nextclade, fastp, samtools_view, bwa_mem |
Variant classification, SNP detection, Validation, Genome indexing, Primer removal, Generation, Read mapping, Variant calling, Sequence contamination filtering, Sequencing quality control, Sequence alignment, Methylation analysis, Tree-based sequence alignment |
|
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 |
2025-12-12 |
4 |
4 |
11.0 |
snpeff_sars_cov_2, picard_MarkDuplicates, lofreq_filter, samtools_stats, multiqc, lofreq_viterbi, lofreq_call, fastp, samtools_view, lofreq_indelqual, bwa_mem |
SNP detection, Validation, Genome indexing, Generation, Read mapping, Sequence contamination filtering, Sequencing quality control, Sequence alignment, Formatting |
|
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 |
2025-12-05 |
2 |
2 |
23.0 |
ivar_consensus, collapse_dataset, __FILTER_FAILED_DATASETS__, ivar_trim, ivar_variants, calculate_numeric_param, __FLATTEN__, lofreq_viterbi, map_param_value, tp_find_and_replace, fastp, samtools_view, bwa_mem, snpSift_extractFields, samtools_stats, multiqc, snpEff_build_gb, pick_value, snpEff, qualimap_bamqc, tp_sed_tool, tp_cat |
Validation, Genome indexing, Primer removal, Read mapping, Generation, Sequence contamination filtering, Sequencing quality control, Sequence alignment |
|
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 |
2026-02-12 |
3 |
3 |
68.0 |
iqtree, ivar_consensus, wc_gnu, Paste1, vapor, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__, collapse_dataset, tp_text_file_with_recurring_lines, __APPLY_RULES__, __MERGE_COLLECTION__, __DUPLICATE_FILE_TO_COLLECTION__, __FILTER_FAILED_DATASETS__, snipit, __FLATTEN__, seqtk_subseq, tp_find_and_replace, __UNZIP_COLLECTION__, rbc_mafft, __RELABEL_FROM_FILE__, fastp, bwa_mem, samtools_view, collection_element_identifiers, Filter1, tp_easyjoin_tool, param_value_from_file, Cut1, Show beginning1, bamtools_split_ref, __FILTER_FROM_FILE__, 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__, qualimap_bamqc, Grep1, tp_cat, __HARMONIZELISTS__ |
De-novo assembly, Base position variability plotting, Sequence analysis, Genome indexing, Primer removal, Read mapping, Generation, Phylogenetic analysis, Sequence file editing, Sequence contamination filtering, Sequencing quality control, Multiple sequence alignment, Data retrieval, Sequence alignment, Data handling, Sequence alignment analysis |
|
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 |
2025-11-27 |
4 |
4 |
40.0 |
EMBOSS: maskseq51, ivar_consensus, __APPLY_RULES__, ivar_trim, __FILTER_FAILED_DATASETS__, datamash_ops, __FLATTEN__, __ZIP_COLLECTION__, fastp, samtools_view, samtools_merge, bwa_mem, collection_element_identifiers, compose_text_param, param_value_from_file, Cut1, samtools_stats, split_file_to_collection, multiqc, fasta_compute_length, qualimap_bamqc, tp_sed_tool, Grep1, tp_cat, __SORTLIST__ |
Sequence analysis, Validation, Genome indexing, Primer removal, Generation, Read mapping, Global alignment, Sequence contamination filtering, Sequencing quality control, Sequence alignment, Sequence alignment analysis, Local alignment |
|
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 |
2025-12-12 |
5 |
5 |
23.0 |
samtools_coverage, snpSift_extractFields, Paste1, clair3, Cut1, bcftools_consensus, Count1, snpSift_filter, minimap2, bcftools_norm, CONVERTER_gz_to_uncompressed, tp_cut_tool, table_compute, tp_head_tool, samtools_depth, collapse_dataset, regexColumn1, Remove beginning1 |
Variant calling, Pairwise sequence alignment |
|
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 |
2025-12-12 |
2 |
2 |
20.0 |
, __MERGE_COLLECTION__, CONVERTER_uncompressed_to_gz, fastq_dl, tp_awk_tool, CONVERTER_gz_to_uncompressed |
|
|
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 |
2025-12-12 |
2 |
2 |
30.0 |
, bedtools_maskfastabed, __FILTER_FROM_FILE__, tp_awk_tool, taxonomy_krona_chart, mapseq, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, k-mer counting, 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 |
2025-12-12 |
2 |
2 |
17.0 |
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, __UNZIP_COLLECTION__, cshl_fasta_formatter, fastp, mgnify_seqprep |
Read pre-processing, Sequence trimming, Validation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence composition calculation |
|
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 |
2025-12-12 |
3 |
3 |
14.0 |
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, cshl_fasta_formatter |
Statistical calculation, Sequence contamination filtering, Sequencing quality control, Read pre-processing, Sequence trimming, Sequence composition calculation, Validation |
|
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 |
2025-12-12 |
2 |
2 |
47.0 |
, bedtools_getfastabed, cmsearch_deoverlap, gops_concat_1, __FILTER_FROM_FILE__, tp_awk_tool, infernal_cmsearch, mapseq, taxonomy_krona_chart, query_tabular, cshl_fasta_formatter, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, Nucleic acid feature detection, k-mer counting, Comparison, Alignment, Mapping |
|
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 |
2025-12-12 |
2 |
2 |
10.0 |
tp_awk_tool, collection_column_join, filter_tabular, query_tabular, Grouping1 |
|
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-discovery/main |
WorkflowHub |
1225 |
https://workflowhub.eu/workflows/1225?version=1 |
Subina Mehta |
|
2024-12-10 |
2025-11-27 |
1 |
1 |
24.0 |
ident_params, fasta_merge_files_and_filter_unique_sequences, Grouping1, Cut1, Grep1, Filter1, msconvert, fasta_cli, maxquant, fasta2tab, tp_cat, search_gui, filter_tabular, query_tabular, Remove beginning1, dbbuilder, peptide_shaker |
Visualisation, Standardisation and normalisation, Imputation, Heat map generation, Filtering, Statistical calculation, Principal component plotting, Protein quantification, Clustering, Formatting |
|
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 |
2025-11-27 |
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 |
2025-11-27 |
1 |
1 |
19.0 |
uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences, Grouping1, Cut1, pepquery2, tp_cat, query_tabular, collapse_dataset, Remove beginning1, dbbuilder, Filter1 |
|
|
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 |
2025-11-27 |
1 |
1 |
3.0 |
fasta_merge_files_and_filter_unique_sequences, metanovo |
Protein identification, Expression analysis, Target-Decoy, de Novo sequencing, Tag-based peptide identification |
|
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 |
2026-01-29 |
1 |
1 |
7.0 |
extract peptides\nCut1, extracting microbial Peptides\nGrep1, maxquant, Quantified-Peptides\nGrouping1, extract proteins\nCut1, extracting microbial Proteins\nGrep1, Quantified-Proteins\nGrouping1 |
Visualisation, Standardisation and normalisation, Imputation, Heat map generation, Statistical calculation, Principal component plotting, Protein quantification, 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 |
2025-12-04 |
12 |
12 |
5.0 |
tooldistillator, bandage_image, bandage_info, shovill, tooldistillator_summarize |
Genome assembly, Data parsing, 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 |
2025-12-12 |
11 |
11 |
8.0 |
kraken2, recentrifuge, tooldistillator, est_abundance, __UNZIP_COLLECTION__, __ZIP_COLLECTION__, tooldistillator_summarize, fastp |
Expression analysis, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Data parsing, Taxonomic classification, Cross-assembly |
|
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 |
2025-12-12 |
2 |
2 |
3.0 |
Rarefaction, Phylogenetic tree for diversity analysis, Taxonomic analysis |
|
|
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 |
2025-11-27 |
1 |
1 |
15.0 |
compose_text_param, param_value_from_file, tab2fasta, abricate, bandage_image, split_file_to_collection, medaka_consensus_pipeline, flye, fasta2tab, tp_find_and_replace, __BUILD_LIST__, collection_element_identifiers |
Mapping assembly, De-novo assembly, Sequence assembly, Base-calling, Antimicrobial resistance prediction, Sequence assembly visualisation, Variant calling, Genome assembly, Cross-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 |
2025-11-27 |
1 |
1 |
60.0 |
bedtools_getfastabed, fasta_merge_files_and_filter_unique_sequences, tab2fasta, Count1, fasta2tab, collapse_dataset, tp_split_on_column, __FILTER_FAILED_DATASETS__, clustalw, fasttree, tp_sorted_uniq, regexColumn1, Cut1, __FILTER_EMPTY_DATASETS__, Remove beginning1, Grouping1, newick_display, tp_replace_in_column, ggplot2_heatmap, tp_multijoin_tool, collection_column_join, regex1 |
Visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation (from molecular sequences), Mapping, 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 |
2025-11-27 |
1 |
1 |
3.0 |
kraken2, krakentools_kreport2krona, taxonomy_krona_chart |
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 |
2025-12-06 |
13 |
13 |
6.0 |
isescan, tooldistillator, plasmidfinder, integron_finder, bakta, tooldistillator_summarize |
Multilocus sequence typing, Structural variation detection, Scaffolding, Genome annotation, Sequence motif recognition, Protein feature detection, Nucleic acid feature detection, Genome assembly, Data parsing |
|
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 |
2025-12-04 |
9 |
9 |
5.0 |
staramr_search, abricate, tooldistillator, amrfinderplus, tooldistillator_summarize |
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 |
2025-12-12 |
3 |
3 |
14.0 |
dada2_filterAndTrim, dada2_mergePairs, dada2_dada, dada2_learnErrors, dada2_makeSequenceTable, dada2_removeBimeraDenovo, dada2_plotQualityProfile, dada2_seqCounts, __UNZIP_COLLECTION__, dada2_assignTaxonomyAddspecies, __APPLY_RULES__ |
Variant calling, DNA barcoding |
|
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 |
create_account, create_or_update, iframe, jbrowse, list_organism |
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 |
qualimap_bamqc, mosdepth, kraken2, tb_profiler_profile, tp_sed_tool, tbvcfreport, bcftools_consensus, tp_awk_tool, __FLATTEN__, multiqc, tb_variant_filter, snippy, fastp, EMBOSS: seqret84 |
Sequence analysis, Validation, Antimicrobial resistance prediction, Variant calling, Global alignment, Sequence contamination filtering, Sequencing quality control, Phylogenetic tree visualisation, Sequence alignment, Taxonomic classification, Phylogenetic tree generation, Sequence alignment analysis, Local alignment |
|
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 |
kraken2, falco, recentrifuge, est_abundance, fastp |
Visualisation, Read mapping, Expression analysis, Statistical calculation, Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Cross-assembly |
|
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 |
kraken2, metaphlan, interactive_tool_phinch, kraken_biom, krakentools_kreport2krona, est_abundance, taxonomy_krona_chart, interactive_tool_pavian, __UNZIP_COLLECTION__ |
Visualisation, Statistical calculation, Aggregation, Genome annotation, Taxonomic classification |
|
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 |
recentrifuge, kraken2, est_abundance |
Statistical calculation, Taxonomic classification, Expression analysis, Cross-assembly |
|
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 |
maxbin2, concoct_coverage_table, semibin, binette, Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, metabat2_jgi_summarize_bam_contig_depths, __BUILD_LIST__, bowtie2, samtools_sort, metabat2, concoct_extract_fasta_bins, concoct, concoct_cut_up_fasta |
Sequence clustering, Sequence assembly, Read binning, Genome annotation, Read mapping |
|
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 |
, bedtools_maskfastabed, __FILTER_FROM_FILE__, tp_awk_tool, taxonomy_krona_chart, mapseq, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, k-mer counting, 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 |
ampvis2_load, tp_awk_tool, collection_column_join, query_tabular, collapse_dataset |
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 |
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, __UNZIP_COLLECTION__, cshl_fasta_formatter, fastp, mgnify_seqprep |
Read pre-processing, Sequence trimming, Validation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence composition calculation |
|
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 |
, __MERGE_COLLECTION__, CONVERTER_uncompressed_to_gz, fastq_dl, tp_awk_tool, CONVERTER_gz_to_uncompressed |
|
|
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 |
tp_awk_tool, collection_column_join, filter_tabular, query_tabular, Grouping1 |
|
|
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 |
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, cshl_fasta_formatter |
Statistical calculation, Sequence contamination filtering, Sequencing quality control, Read pre-processing, Sequence trimming, Sequence composition calculation, Validation |
|
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, cmsearch_deoverlap, gops_concat_1, __FILTER_FROM_FILE__, tp_awk_tool, infernal_cmsearch, mapseq, taxonomy_krona_chart, query_tabular, cshl_fasta_formatter, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, Nucleic acid feature detection, k-mer counting, Comparison, Alignment, Mapping |
|
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 |
combine_metaphlan2_humann2, Cut1, Grep1, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, tp_find_and_replace, humann_unpack_pathways, humann_rename_table |
Phylogenetic analysis, Species frequency estimation, Taxonomic classification |
|
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 |
phyloseq_from_dada2, dada2_filterAndTrim, dada2_dada, dada2_learnErrors, tp_replace_in_column, tp_replace_in_line, dada2_makeSequenceTable, dada2_removeBimeraDenovo, dada2_plotQualityProfile, dada2_seqCounts, cat1, collection_element_identifiers, __UNZIP_COLLECTION__, __SORTLIST__, dada2_assignTaxonomyAddspecies, Add_a_column1, tp_head_tool, dada2_mergePairs |
Visualisation, Variant calling, DNA barcoding, Analysis, Deposition |
|
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 |
cutadapt, humann_unpack_pathways, humann, graphlan, metaphlan, fastqc, tp_find_and_replace, export2graphlan, Cut1, combine_metaphlan_humann, multiqc, taxonomy_krona_chart, humann_renorm_table, bg_sortmerna, Grouping1, tp_sort_header_tool, fastq_paired_end_interlacer, Grep1, humann_split_stratified_table, humann_regroup_table, graphlan_annotate, humann_rename_table |
Species frequency estimation, Sequence comparison, Conversion, Validation, Primer removal, Phylogenetic tree editing, Phylogenetic analysis, Statistical calculation, Phylogenetic tree visualisation, Sequence composition calculation, Sequence alignment analysis, Visualisation, Sequence similarity search, Aggregation, Read pre-processing, Sequence trimming, Phylogenetic inference, Sequencing quality control, Taxonomic classification |
|
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, Cut1, taxonomy_krona_chart, graphlan_annotate, export2graphlan |
Visualisation, Conversion, Phylogenetic tree editing, Phylogenetic inference, Phylogenetic tree visualisation, Taxonomic classification |
|
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 |
cutadapt, fastq_paired_end_interlacer, fastqc, multiqc, bg_sortmerna |
Sequence similarity search, Sequence comparison, Read pre-processing, Sequence trimming, Validation, Primer removal, Statistical calculation, Sequencing quality control, Sequence composition calculation, Sequence alignment analysis |
|
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 |
tp_sort_header_tool, Grep1, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, tp_find_and_replace, humann_unpack_pathways, humann_rename_table, humann |
Phylogenetic analysis, Species frequency estimation, Taxonomic classification |
|
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 |
coverm_contig, bandage_image, bandage_info, collection_column_join, megahit, metaspades, bowtie2, megahit_contig2fastg, quast |
Visualisation, Local alignment, Genome assembly, Sequence assembly validation, Read mapping, 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, cshl_fastq_to_fasta, Count1, 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 |
kraken2, falco, recentrifuge, est_abundance, fastp |
Visualisation, Read mapping, Expression analysis, Statistical calculation, Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Cross-assembly |
|
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 |
EMBOSS: maskseq51, compose_text_param, param_value_from_file, Cut1, Grep1, datamash_ops, Add_a_column1, fasta_compute_length |
Global alignment, Sequence analysis, Sequence alignment, Sequence alignment analysis, Local alignment |
|
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 |
racon, staramr_search, miniasm, bandage_image, gfa_to_fa, minimap2, unicycler, PlasFlow, nanoplot |
Mapping assembly, De-novo assembly, Aggregation, Sequence analysis, Scatter plot plotting, Antimicrobial resistance prediction, Sequence assembly visualisation, Pairwise sequence alignment, Box-Whisker plot plotting, Genome 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_make_biom, mothur_summary_seqs, mothur_make_shared, mothur_classify_seqs, krona-text, mothur_make_group, mothur_screen_seqs, mothur_align_seqs, mothur_count_seqs, mothur_cluster_split, mothur_classify_otu, mothur_pre_cluster, mothur_filter_seqs, mothur_merge_files, mothur_unique_seqs |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
kraken2, tp_replace_in_line, fastqc, porechop, datamash_reverse, multiqc, taxonomy_krona_chart, fastp, Remove beginning1 |
Visualisation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Validation, Sequence composition calculation, Taxonomic classification |
|
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 |
metaphlan2krona, humann2_regroup_table, taxonomy_krona_chart, metaphlan2, humann2, humann2_renorm_table |
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 |
tp_tail_tool, tp_replace_in_column, Cut1, count_gff_features, tab2fasta, ggplot2_histogram, cat1, minimap2, sort1, CONVERTER_fasta_to_tabular, add_column_headers, Add_a_column1, histogram_rpy, tp_sorted_uniq, join1, Filter1, Grouping1, MQoutputfilter |
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_summary_seqs, mothur_dist_seqs, mothur_screen_seqs, mothur_taxonomy_to_krona, mothur_classify_otu, mothur_tree_shared, mothur_venn, mothur_make_biom, mothur_heatmap_sim, mothur_remove_seqs, mothur_remove_groups, mothur_cluster, mothur_make_shared, mothur_dist_shared, mothur_align_seqs, mothur_cluster_split, taxonomy_krona_chart, XY_Plot_1, mothur_filter_seqs, mothur_seq_error, mothur_sub_sample, mothur_summary_single, mothur_unique_seqs, newick_display, mothur_rarefaction_single, mothur_classify_seqs, mothur_count_groups, mothur_count_seqs, mothur_pre_cluster, mothur_get_groups, mothur_remove_lineage, mothur_make_contigs, mothur_chimera_vsearch |
Visualisation, DNA barcoding, Phylogenetic tree analysis, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Phylogenetic tree reconstruction, Taxonomic classification, Phylogenetic tree generation |
|
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, fastqc, porechop, krakentools_kreport2krona, taxonomy_krona_chart, fastp, Filter1 |
Visualisation, Statistical calculation, Aggregation, Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification |
|
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, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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_screen_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_count_seqs |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
newick_display, mothur_heatmap_sim, mothur_dist_shared, mothur_tree_shared, mothur_venn, collapse_dataset |
Visualisation, DNA barcoding, Phylogenetic tree analysis, Sequence read processing, Phylogenetic analysis, Sequence clustering, Phylogenetic tree reconstruction, Sequencing quality control, Taxonomic classification, Phylogenetic tree generation |
|
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_summary_single, mothur_rarefaction_single |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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_cluster, mothur_make_shared, mothur_dist_seqs, mothur_rarefaction_single |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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_make_shared, mothur_count_groups, mothur_cluster_split, mothur_classify_otu, mothur_sub_sample, mothur_remove_groups |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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_summary_seqs, mothur_screen_seqs, mothur_pre_cluster, mothur_remove_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_chimera_vsearch |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2023-02-13 |
1 |
1 |
12.0 |
racon, staramr_search, miniasm, bandage_image, gfa_to_fa, minimap2, unicycler, PlasFlow, nanoplot |
Mapping assembly, De-novo assembly, Aggregation, Sequence analysis, Scatter plot plotting, Antimicrobial resistance prediction, Sequence assembly visualisation, Pairwise sequence alignment, Box-Whisker plot plotting, Genome 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 |
2023-02-13 |
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 |
2023-02-13 |
1 |
1 |
7.0 |
ncbi_blastn_wrapper, fasta_merge_files_and_filter_unique_sequences, samtools_stats, picard_SamToFastq, minimap2, ngsutils_bam_filter, shovill |
Variant calling, Sequence contamination filtering, Pairwise sequence alignment, Read pre-processing, Sequencing quality control, Genome assembly, Formatting |
|
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 |
2023-02-13 |
1 |
1 |
3.0 |
taxonomy_krona_chart, kraken2, Kraken2Tax |
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 |
2023-02-13 |
1 |
1 |
3.0 |
taxonomy_krona_chart, kraken2, Kraken2Tax |
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 |
2026-03-02 |
1 |
1 |
19.0 |
tp_easyjoin_tool, tabular_to_csv, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2_core__tools__import, qiime2__feature_table__summarize, qiime_extract_viz, csv_to_tabular, qiime2_core__tools__export, qiime2__feature_table__tabulate_seqs, qiime2__taxa__barplot, qiime2__feature_classifier__extract_reads, Remove beginning1, biom_convert, qiime2__feature_classifier__classify_sklearn |
Visualisation, Demultiplexing, Taxonomic classification, Formatting |
Taxonomy |
CC-BY-4.0 |
10.48546/workflowhub.workflow.2098.1 |
Melbourne Bioinformatics |
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 |
Extract column name and fraction_total_reads from Bracken report\nCut1, kraken2, add_line_to_file, cat_multiple, krakentools_kreport2krona, est_abundance, collection_column_join, taxonomy_krona_chart, regex1, krakentools_alpha_diversity, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, krakentools_combine_kreports, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, krakentools_beta_diversity, __RELABEL_FROM_FILE__, Prepare alpha diversity summary file\nPaste1, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1, collection_element_identifiers |
Visualisation, Statistical calculation, Aggregation, Taxonomic classification |
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 |
2024-04-05 |
1 |
1 |
17.0 |
, metaphlan2krona, merge_metaphlan_tables, Cut1, humann2_renorm_table, taxonomy_krona_chart, metaphlan2, humann2, humann2_regroup_table |
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 |
2023-11-09 |
1 |
1 |
4.0 |
newick_display, mothur_tree_shared, mothur_heatmap_sim, mothur_dist_shared |
Visualisation, DNA barcoding, Phylogenetic tree analysis, Sequence read processing, Phylogenetic analysis, Sequence clustering, Phylogenetic tree reconstruction, Sequencing quality control, Taxonomic classification, Phylogenetic tree generation |
|
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 |
2023-11-09 |
1 |
1 |
3.0 |
XY_Plot_1, mothur_summary_single, mothur_rarefaction_single |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2023-11-09 |
1 |
1 |
5.0 |
mothur_make_shared, mothur_count_groups, mothur_cluster_split, mothur_classify_otu, mothur_sub_sample |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2023-11-09 |
1 |
1 |
2.0 |
mothur_classify_seqs, mothur_remove_lineage |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2023-11-09 |
1 |
1 |
5.0 |
mothur_screen_seqs, mothur_summary_seqs, mothur_unique_seqs, mothur_count_seqs |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2023-11-09 |
1 |
1 |
9.0 |
mothur_summary_seqs, mothur_screen_seqs, mothur_pre_cluster, mothur_remove_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_chimera_vsearch |
Visualisation, DNA barcoding, Phylogenetic analysis, Sequence clustering, Sequencing quality control, Sequence read processing, Taxonomic classification |
|
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 |
2024-06-12 |
1 |
1 |
15.0 |
qualimap_bamqc, mosdepth, kraken2, tb_profiler_profile, tp_sed_tool, tbvcfreport, bcftools_consensus, tp_awk_tool, __FLATTEN__, multiqc, tb_variant_filter, snippy, fastp, EMBOSS: seqret84 |
Sequence analysis, Validation, Antimicrobial resistance prediction, Variant calling, Global alignment, Sequence contamination filtering, Sequencing quality control, Phylogenetic tree visualisation, Sequence alignment, Taxonomic classification, Phylogenetic tree generation, Sequence alignment analysis, Local alignment |
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 |
2024-09-09 |
1 |
1 |
14.0 |
hamronize_summarize, srst2, seqsero2, hamronize_tool, kma_map, bbtools_tadpole, sistr_cmd, mob_recon, bbtools_bbduk, __UNZIP_COLLECTION__, shovill |
Multilocus sequence typing, Sequence analysis, Read mapping, Sequence contamination filtering, Clustering, Data handling, Visualisation, Genome alignment, Sequence trimming, Genome indexing, Antimicrobial resistance prediction, Parsing, Read binning, Sequence alignment, Genome assembly, RNA-Seq analysis |
|
GPL-3.0 |
|
Seq4AMR |
True |
False |
|
Workflow 2: Sciensano |
WorkflowHub |
644 |
https://workflowhub.eu/workflows/644?version=1 |
|
|
2023-11-07 |
2024-09-09 |
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 |
2024-09-09 |
1 |
1 |
10.0 |
hamronize_summarize, staramr_search, hamronize_tool, abricate, tp_find_and_replace, shovill, collapse_dataset |
Data handling, Genome assembly, Antimicrobial resistance prediction, Parsing |
|
GPL-3.0 |
|
Seq4AMR |
True |
False |
|
Workflow 1: AbritAMR |
WorkflowHub |
634 |
https://workflowhub.eu/workflows/634?version=1 |
|
|
2023-10-31 |
2024-09-09 |
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 |
2024-12-24 |
2 |
2 |
36.0 |
, hamronize_summarize, staramr_search, cast, shovill, collapse_dataset, tp_split_on_column, tp_text_file_with_recurring_lines, __APPLY_RULES__, __MERGE_COLLECTION__, abricate, datamash_ops, tp_find_and_replace, Cut1, cat_multi_datasets, addValue, hamronize_tool, Grep1, cat1 |
Data handling, Genome assembly, Antimicrobial resistance prediction, Parsing |
|
MIT |
|
Seq4AMR, ErasmusMC Clinical Bioinformatics |
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 |
|
kraken2, tp_replace_in_line, fastqc, porechop, datamash_reverse, multiqc, taxonomy_krona_chart, fastp, Remove beginning1 |
Visualisation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Validation, Sequence composition calculation, Taxonomic classification |
|
|
|
|
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 |
|
trim_galore, fasplit, maxbin2, fastqc, coverm_contig, tp_grep_tool, fraggenescan, cat_bins, checkm_lineage_wf, tp_awk_tool, tp_cat, interproscan, hmmer_hmmscan, coverm_genome, sort1, quast |
Sequence assembly, Conversion, Validation, Primer removal, Sequence profile generation, Sequence generation, Coding region prediction, Statistical calculation, Multiple sequence alignment, Format validation, Sequence composition calculation, Sequence assembly validation, Formatting, Visualisation, Sequence database search, Gene prediction, Read pre-processing, Sequence trimming, Database search, Probabilistic sequence generation, Sequence motif recognition, Protein feature detection, Sequencing quality control, Data retrieval, Taxonomic classification, Local alignment |
|
|
|
|
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 |
|
kraken2, metaphlan2krona, metaphlan, add_line_to_file, krakentools_kreport2krona, est_abundance, taxonomy_krona_chart, datamash_transpose, cat1, sylph_profile, Remove beginning1, taxpasta, collection_element_identifiers |
Visualisation, Statistical calculation, Aggregation, Standardisation and normalisation, Conversion, Taxonomic classification, Formatting |
|
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 |
|
__MERGE_COLLECTION__, __FLATTEN__, multiqc, regex1, checkm2, __RELABEL_FROM_FILE__, collection_element_identifiers |
Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation |
|
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 |
|
maaslin2, unzip, tp_cut_tool, mmuphin, ampvis2_subset_samples, phyloseq_from_biom, ampvis2_heatmap, fastqc, calculate_numeric_param, __FLATTEN__, tp_awk_tool, datamash_transpose, ampvis2_export_otu, biom_convert, compose_text_param, tp_easyjoin_tool, param_value_from_file, ampvis2_load, multiqc, decontam, lotus2, volcanoplot, Remove beginning1, phyloseq_add_rank_names, ampvis2_ordinate, phyloseq_tax_glom, regex1, bg_column_arrange_by_header |
Visualisation, Standardisation and normalisation, DNA barcoding, Validation, Sequence feature detection, Filtering, Analysis, Deposition, Statistical calculation, Sequencing quality control, Classification, Sequence composition calculation, Formatting |
|
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 |
|
kraken2, humann_unpack_pathways, collapse_dataset, tp_text_file_with_recurring_lines, humann, add_line_to_file, metaphlan, csv_to_tabular, tp_awk_tool, datamash_transpose, __UNZIP_COLLECTION__, krakentools_alpha_diversity, taxpasta, collection_element_identifiers, tp_easyjoin_tool, krakentools_kreport2krona, taxonomy_krona_chart, humann_renorm_table, sylph_profile, Remove beginning1, tp_sed_tool, tp_replace_in_line, fastq_paired_end_interlacer, est_abundance, humann_regroup_table, cat1, collection_column_join, humann_rename_table, sort1 |
Visualisation, Species frequency estimation, Standardisation and normalisation, Aggregation, Conversion, Phylogenetic analysis, Statistical calculation, Taxonomic classification, Formatting |
|
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 |
|
rna_star, __FILTER_FAILED_DATASETS__, featurecounts, fastqc, multiqc, collection_column_join, umi_tools_extract, umi_tools_dedup |
Statistical calculation, RNA-Seq quantification, Sequencing quality control, Validation, Sequence alignment, Sequence composition calculation, Read summarisation |
|
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 |
|
trim_galore, kofamscan, fasplit, maxbin2, fastqc, coverm_contig, tp_grep_tool, fraggenescan, cat_bins, checkm_lineage_wf, tp_awk_tool, tp_cat, interproscan, hmmer_hmmscan, coverm_genome, sort1, quast |
Sequence assembly, Sequence analysis, Validation, Conversion, Primer removal, Sequence profile generation, Sequence generation, Gene functional annotation, Statistical calculation, Coding region prediction, Multiple sequence alignment, Format validation, Sequence composition calculation, Sequence assembly validation, Formatting, Visualisation, Sequence database search, Gene prediction, Read pre-processing, Sequence trimming, Database search, Probabilistic sequence generation, Sequence motif recognition, Protein feature detection, Sequencing quality control, Data retrieval, Taxonomic classification, Local alignment |
|
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 |
|
cutadapt, metaphlan2, graphlan, combine_metaphlan2_humann2, metaphlan2krona, fastqc, export2graphlan, humann2, humann2_unpack_pathways, format_metaphlan2_output, multiqc, taxonomy_krona_chart, group_humann2_uniref_abundances_to_go, humann2_genefamilies_genus_level, bg_sortmerna, humann2_renorm_table, Grouping1, tp_sort_header_tool, fastq_paired_end_interlacer, Grep1, graphlan_annotate |
Sequence comparison, Conversion, Validation, Phylogenetic tree editing, Primer removal, Statistical calculation, Phylogenetic tree visualisation, Sequence composition calculation, Formatting, Sequence alignment analysis, Visualisation, Sequence similarity search, Read pre-processing, Sequence trimming, Phylogenetic inference, Sequencing quality control, Taxonomic classification |
|
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 |
|
trim_galore, fastqc, kallisto_quant, collection_column_join, __UNZIP_COLLECTION__, bg_sortmerna |
Sequence similarity search, Sequence comparison, Read pre-processing, Sequence trimming, Primer removal, Statistical calculation, Sequencing quality control, Sequence composition calculation, Sequence alignment analysis, Gene expression profiling |
|
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 |
|
bg_diamond, Cut1, gops_intersect_1, tab2fasta, collapse_dataset, bg_diamond_view, cat1, rapidnj, Add_a_column1, rbc_mafft, join1, tp_split_on_column, regexColumn1, Filter1 |
Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment |
|
|
|
|
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 |
|
peptide_shaker, sqlite_to_tabular, search_gui, 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, __EXTRACT_DATASET__, map_param_value, __BUILD_LIST__, __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 |
|
flashlfq, tp_replace_in_column, unipept, tp_replace_in_line, Cut1, Filter1, msconvert, regex1, search_gui, query_tabular, Remove beginning1, peptide_shaker |
Visualisation, Prediction and recognition, Label-free quantification, 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_sample, metaquantome_viz, metaquantome_filter, metaquantome_db, metaquantome_stat, metaquantome_expand |
Principal component visualisation, Quantification, Heat map generation, Indexing, Differential protein expression analysis, Visualisation, Statistical inference, Query and retrieval, 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 |
|
recentrifuge, kraken2, fastq_to_tabular, filter_tabular, seq_filter_by_id, bowtie2 |
Read mapping, Taxonomic classification, Expression analysis, Cross-assembly |
|
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 |
|
bowtie2, multiqc, featurecounts |
RNA-Seq quantification, Sequencing quality control, Validation, Read summarisation, Read mapping |
|
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, multiqc, fastqc |
Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation |
|
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 |
|
__BUILD_LIST__, interactive_tool_jupyter_notebook |
|
|
|
|
|
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 |
|
tp_grep_tool, bedtools_sortbed, bedtools_complementbed, collapse_dataset, bedtools_intersectbed, datamash_ops, lastz_wrapper_2, Filter1, random_lines1, Cut1, mergeCols1, fasta_compute_length, join1, addValue, tp_sort_header_tool, tp_sed_tool, Grep1, fasta_filter_by_length, cat1, tp_cat |
Sequence alignment, Mapping, Read 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 |
|
bg_diamond, Cut1, gops_intersect_1, tab2fasta, collapse_dataset, bg_diamond_view, cat1, rapidnj, Add_a_column1, rbc_mafft, join1, tp_split_on_column, regexColumn1, Filter1 |
Phylogenetic tree generation, Sequence alignment analysis, Multiple sequence alignment |
|
|
|
|
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 |
|
create_account, create_or_update, iframe, jbrowse, list_organism |
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 |
|
staramr_search, tab2fasta, circos, medaka_consensus_pipeline, flye, circos_interval_to_tile, jbrowse, fasta2tab, tp_cut_tool, Add_a_column1, tp_head_tool, PlasFlow, tp_split_on_column, tp_text_file_with_recurring_lines, nanoplot, tbl2gff3, bandage_image, minimap2, prokka, Filter1, tp_easyjoin_tool, Cut1, trimmomatic, deeptools_bam_coverage, fasta_compute_length, join1, gff2bed1, ncbi_blastn_wrapper, circos_wiggle_to_scatter, circos_gc_skew, tp_sort_header_tool, Grep1, regex1, tp_cat, regex_replace, bg_column_arrange_by_header |
De-novo assembly, Sequence assembly, Sequence analysis, Base-calling, Sequence assembly visualisation, Variant calling, Coding region prediction, Genome assembly, Genome visualisation, Scatter plot plotting, Box-Whisker plot plotting, Pairwise sequence alignment, Cross-assembly, Mapping assembly, Gene prediction, Antimicrobial resistance prediction, Sequence visualisation, Genome annotation |
|
|
|
|
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, tp_cat, tb_variant_filter, 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 |
|
__MERGE_COLLECTION__, snippy, trimmomatic, tb_variant_filter |
Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation |
|
|
|
|
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 |
|
__MERGE_COLLECTION__, tb_profiler_profile, tp_sed_tool, tp_replace_in_line, tp_grep_tool, tp_cat, addName, samtools_view |
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 |
|
freebayes, bcftools_view, vcf2tsv, tp_awk_tool, snpSift_filter, bcftools_norm, bowtie2 |
Variant calling, Statistical calculation, Read mapping |
|
|
|
|
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 |
|
samtools_coverage, samtools_depth, freebayes, vcf2tsv, bcftools_norm, tp_cat, bowtie2, collapse_dataset, collection_element_identifiers |
Variant calling, Statistical calculation, Read mapping |
|
|
|
|
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 |
|
__MERGE_COLLECTION__, __FLATTEN__, multiqc, regex1, checkm2, __RELABEL_FROM_FILE__, collection_element_identifiers |
Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation |
|
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 |
|
__MERGE_COLLECTION__, __FLATTEN__, multiqc, regex1, checkm2, __RELABEL_FROM_FILE__, collection_element_identifiers |
Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation |
|
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 |
|
__MERGE_COLLECTION__, CONVERTER_uncompressed_to_gz, fastq_dl, tp_awk_tool, CONVERTER_gz_to_uncompressed |
|
|
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 |
|
bedtools_maskfastabed, __FILTER_FROM_FILE__, tp_awk_tool, taxonomy_krona_chart, mapseq, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, k-mer counting, 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 |
|
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, __UNZIP_COLLECTION__, cshl_fasta_formatter, fastp, mgnify_seqprep |
Read pre-processing, Sequence trimming, Validation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence composition calculation |
|
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 |
|
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, cshl_fasta_formatter |
Statistical calculation, Sequence contamination filtering, Sequencing quality control, Read pre-processing, Sequence trimming, Sequence composition calculation, Validation |
|
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 |
|
samtools_coverage, snpSift_extractFields, Paste1, clair3, Cut1, bcftools_consensus, Count1, snpSift_filter, minimap2, bcftools_norm, CONVERTER_gz_to_uncompressed, tp_cut_tool, table_compute, tp_head_tool, samtools_depth, collapse_dataset, regexColumn1, Remove beginning1 |
Variant calling, Pairwise sequence alignment |
|
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 |
|
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, cshl_fasta_formatter |
Statistical calculation, Sequence contamination filtering, Sequencing quality control, Read pre-processing, Sequence trimming, Sequence composition calculation, Validation |
|
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 |
|
samtools_coverage, snpSift_extractFields, Paste1, clair3, Cut1, bcftools_consensus, Count1, snpSift_filter, minimap2, bcftools_norm, CONVERTER_gz_to_uncompressed, tp_cut_tool, table_compute, tp_head_tool, samtools_depth, collapse_dataset, regexColumn1, Remove beginning1 |
Variant calling, Pairwise sequence alignment |
|
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 |
|
__MERGE_COLLECTION__, CONVERTER_uncompressed_to_gz, fastq_dl, tp_awk_tool, CONVERTER_gz_to_uncompressed |
|
|
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 |
|
bedtools_maskfastabed, __FILTER_FROM_FILE__, tp_awk_tool, taxonomy_krona_chart, mapseq, __FILTER_EMPTY_DATASETS__, biom_convert, collection_element_identifiers |
Visualisation, Formatting, k-mer counting, 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 |
|
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, __UNZIP_COLLECTION__, cshl_fasta_formatter, fastp, mgnify_seqprep |
Read pre-processing, Sequence trimming, Validation, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Nucleic acid design, Sequence composition calculation |
|
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 |
|
fastq_to_fasta_python, prinseq, fastq_filter, fastqc, trimmomatic, multiqc, tp_find_and_replace, cshl_fasta_formatter |
Statistical calculation, Sequence contamination filtering, Sequencing quality control, Read pre-processing, Sequence trimming, Sequence composition calculation, Validation |
|
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 |
|
__FILTER_FAILED_DATASETS__, kraken2, bamtools_split_mapped, fastqc, porechop, Grep1, Cut1, krakentools_extract_kraken_reads, multiqc, samtools_fastx, minimap2, collection_column_join, Add_a_column1, collapse_dataset, regexColumn1, fastp, nanoplot |
Visualisation, Aggregation, Validation, Scatter plot plotting, Taxonomic classification, Statistical calculation, Sequence contamination filtering, Sequencing quality control, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence composition calculation, Data handling, Sequence alignment analysis |
|
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 |
|
__MERGE_COLLECTION__, __FLATTEN__, multiqc, regex1, checkm2, __RELABEL_FROM_FILE__, collection_element_identifiers |
Statistical calculation, Sequencing quality control, Validation, Sequence composition calculation, Sequence assembly validation |
|
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 |
|
samtools_coverage, snpSift_extractFields, Paste1, clair3, Cut1, bcftools_consensus, Count1, snpSift_filter, minimap2, bcftools_norm, CONVERTER_gz_to_uncompressed, tp_cut_tool, table_compute, tp_head_tool, samtools_depth, collapse_dataset, regexColumn1, Remove beginning1 |
Variant calling, Pairwise sequence alignment |
|
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 |
|
samtools_coverage, snpSift_extractFields, Paste1, clair3, Cut1, bcftools_consensus, Count1, snpSift_filter, minimap2, bcftools_norm, CONVERTER_gz_to_uncompressed, tp_cut_tool, table_compute, tp_head_tool, samtools_depth, collapse_dataset, regexColumn1, Remove beginning1 |
Variant calling, Pairwise sequence alignment |
|
MIT |
|
|
True |
False |