|
metagenomic-raw-reads-amr-analysis/main |
WorkflowHub |
2068 |
https://workflowhub.eu/workflows/2068?version=1 |
ABRomics None, Hugo Lefeuvre |
|
2026-01-24 |
2026-01-25 |
1 |
1 |
20.0 |
sylph_profile, deeparg_short_reads, collection_element_identifiers, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, fastq_paired_end_interlacer, table_pandas_rename_column, multiqc, groot, tp_text_file_with_recurring_lines, tooldistillator, Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__, tooldistillator_summarize, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, __RELABEL_FROM_FILE__, argnorm, __FILTER_FAILED_DATASETS__, __UNZIP_COLLECTION__ |
Validation, Gene functional annotation, Sequencing quality control, Antimicrobial resistance prediction, Data parsing, 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=1 |
ABRomics None, Clea Siguret, Hugo Lefeuvre |
|
2026-01-21 |
2026-01-25 |
1 |
1 |
3.0 |
coreprofiler_allele_calling, tooldistillator, tooldistillator_summarize |
Data parsing, Multilocus sequence typing |
|
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, collapse_dataset, pick_value, est_abundance, quast, tooldistillator, tooldistillator_summarize, recentrifuge, checkm2 |
Validation, Sequencing quality control, Sequence composition calculation, Data parsing, Taxonomic classification, Sequence assembly validation, Statistical calculation, Cross-assembly, Expression analysis, Visualisation |
|
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=6 |
Peter van Heusden |
virology |
2025-07-31 |
2026-01-25 |
6 |
6 |
16.0 |
qualimap_bamqc, snpeff_sars_cov_2, multiqc, samtools_view, __FLATTEN__, ivar_consensus, fastp, nextclade, ivar_trim, pangolin, samtools_stats, bwa_mem, tp_sed_tool, tp_cat, ivar_variants |
SNP detection, Validation, Tree-based sequence alignment, Sequencing quality control, Primer removal, Genome indexing, Read mapping, Variant calling, Generation, Sequence contamination filtering, Variant classification, Sequence alignment, Methylation analysis |
|
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, multiqc, samtools_view, picard_MarkDuplicates, fastp, lofreq_indelqual, lofreq_call, lofreq_viterbi, samtools_stats, bwa_mem, lofreq_filter |
SNP detection, Formatting, Validation, Sequencing quality control, Genome indexing, Read mapping, Generation, Sequence contamination filtering, Sequence alignment |
|
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 |
samtools_view, ivar_consensus, snpEff, ivar_trim, lofreq_viterbi, __FILTER_FAILED_DATASETS__, calculate_numeric_param, qualimap_bamqc, multiqc, pick_value, __FLATTEN__, map_param_value, fastp, bwa_mem, tp_find_and_replace, tp_cat, snpEff_build_gb, collapse_dataset, samtools_stats, tp_sed_tool, snpSift_extractFields, ivar_variants |
Validation, Sequencing quality control, Primer removal, Genome indexing, Read mapping, Generation, Sequence contamination filtering, 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=2 |
Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin |
virology |
2025-05-14 |
2025-12-12 |
2 |
2 |
68.0 |
seqtk_subseq, rbc_mafft, __FILTER_FROM_FILE__, samtools_view, ivar_consensus, bamtools_split_ref, wc_gnu, __HARMONIZELISTS__, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__, __FILTER_FAILED_DATASETS__, Cut1, qualimap_bamqc, collection_element_identifiers, __FLATTEN__, Grep1, fastp, tp_text_file_with_recurring_lines, __RELABEL_FROM_FILE__, snipit, bwa_mem, tp_find_and_replace, tp_cat, __MERGE_COLLECTION__, param_value_from_file, Filter1, iqtree, __DUPLICATE_FILE_TO_COLLECTION__, tp_easyjoin_tool, collapse_dataset, Show beginning1, Paste1, 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__, __APPLY_RULES__, __UNZIP_COLLECTION__, vapor |
Sequence analysis, Multiple sequence alignment, Sequencing quality control, Primer removal, Base position variability plotting, Genome indexing, Read mapping, Generation, De-novo assembly, Data handling, Sequence contamination filtering, Sequence file editing, Phylogenetic analysis, Sequence alignment, Sequence alignment analysis, Data retrieval |
|
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 |
__ZIP_COLLECTION__, samtools_view, ivar_consensus, ivar_trim, __FILTER_FAILED_DATASETS__, Cut1, qualimap_bamqc, multiqc, collection_element_identifiers, datamash_ops, Grep1, __FLATTEN__, fastp, fasta_compute_length, bwa_mem, samtools_merge, tp_cat, param_value_from_file, split_file_to_collection, compose_text_param, EMBOSS: maskseq51, samtools_stats, tp_sed_tool, __APPLY_RULES__, __SORTLIST__ |
Validation, Sequence analysis, Sequencing quality control, Primer removal, Genome indexing, Read mapping, Generation, Global alignment, Sequence contamination filtering, Local alignment, Sequence alignment, Sequence alignment analysis |
|
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 |
Cut1, Remove beginning1, collapse_dataset, Count1, bcftools_consensus, snpSift_extractFields, bcftools_norm, tp_cut_tool, CONVERTER_gz_to_uncompressed, table_compute, clair3, regexColumn1, samtools_coverage, minimap2, samtools_depth, tp_head_tool, Paste1, snpSift_filter |
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 |
2025-12-12 |
2 |
2 |
20.0 |
, __MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz, fastq_dl |
|
|
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 |
, collection_element_identifiers, __FILTER_FROM_FILE__, tp_awk_tool, __FILTER_EMPTY_DATASETS__, mapseq, bedtools_maskfastabed, biom_convert, taxonomy_krona_chart |
Mapping, Visualisation, Formatting, k-mer counting |
|
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 |
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastp, fastqc, mgnify_seqprep, trimmomatic, tp_find_and_replace, __UNZIP_COLLECTION__ |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing, Nucleic acid design |
|
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 |
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastqc, trimmomatic, tp_find_and_replace |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing |
|
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 |
, collection_element_identifiers, cshl_fasta_formatter, __FILTER_FROM_FILE__, tp_awk_tool, gops_concat_1, cmsearch_deoverlap, infernal_cmsearch, __FILTER_EMPTY_DATASETS__, mapseq, query_tabular, biom_convert, bedtools_getfastabed, taxonomy_krona_chart |
Mapping, Comparison, Formatting, Alignment, k-mer counting, Nucleic acid feature detection, Visualisation |
|
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 |
Cut1, Remove beginning1, fasta_cli, ident_params, maxquant, Grep1, Filter1, tp_cat, msconvert, fasta2tab, fasta_merge_files_and_filter_unique_sequences, search_gui, filter_tabular, query_tabular, Grouping1, dbbuilder, peptide_shaker |
Principal component plotting, Formatting, Imputation, Clustering, Filtering, Statistical calculation, Heat map generation, Protein quantification, Standardisation and normalisation, Visualisation |
|
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 |
unipept, Grep1, msstatstmt |
Prediction and recognition, Visualisation |
|
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 |
Cut1, Remove beginning1, uniprotxml_downloader, collapse_dataset, Filter1, fasta_merge_files_and_filter_unique_sequences, query_tabular, tp_cat, Grouping1, dbbuilder, pepquery2 |
|
|
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 |
de Novo sequencing, Protein identification, Tag-based peptide identification, Target-Decoy, Expression analysis |
|
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, maxquant, extracting microbial Proteins\nGrep1, extract proteins\nCut1, Quantified-Proteins\nGrouping1, Quantified-Peptides\nGrouping1, extracting microbial Peptides\nGrep1 |
Principal component plotting, Imputation, Clustering, Statistical calculation, Heat map generation, Protein quantification, Standardisation and normalisation, Visualisation |
|
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 |
bandage_info, tooldistillator, tooldistillator_summarize, bandage_image, shovill |
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, __ZIP_COLLECTION__, est_abundance, tooldistillator, fastp, tooldistillator_summarize, recentrifuge, __UNZIP_COLLECTION__ |
Sequence contamination filtering, Statistical calculation, Cross-assembly, Sequencing quality control, Data parsing, Taxonomic classification, Expression analysis |
|
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 |
Taxonomic analysis, Rarefaction, Phylogenetic tree for diversity 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 |
collection_element_identifiers, param_value_from_file, abricate, tp_find_and_replace, split_file_to_collection, bandage_image, fasta2tab, medaka_consensus_pipeline, flye, __BUILD_LIST__, compose_text_param, tab2fasta |
Mapping assembly, Base-calling, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Genome assembly, Sequence assembly visualisation, Cross-assembly, Sequence 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 |
Remove beginning1, regexColumn1, fasttree, __FILTER_FAILED_DATASETS__, Cut1, Count1, collection_column_join, fasta_merge_files_and_filter_unique_sequences, __FILTER_EMPTY_DATASETS__, Grouping1, tp_multijoin_tool, ggplot2_heatmap, tp_replace_in_column, tp_sorted_uniq, bedtools_getfastabed, clustalw, collapse_dataset, tab2fasta, tp_split_on_column, fasta2tab, regex1, newick_display |
Mapping, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multiple sequence alignment, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Visualisation |
|
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 |
Aggregation, Taxonomic classification, Visualisation |
|
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, integron_finder, tooldistillator, tooldistillator_summarize, bakta, plasmidfinder |
Genome annotation, Protein feature detection, Structural variation detection, Data parsing, Multilocus sequence typing, Genome assembly, Scaffolding, Nucleic acid feature detection, Sequence motif recognition |
|
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 |
Antimicrobial resistance prediction, Data parsing |
|
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_assignTaxonomyAddspecies, dada2_plotQualityProfile, dada2_makeSequenceTable, dada2_mergePairs, dada2_removeBimeraDenovo, dada2_seqCounts, dada2_filterAndTrim, dada2_learnErrors, __APPLY_RULES__, dada2_dada, __UNZIP_COLLECTION__ |
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 |
list_organism, create_account, create_or_update, jbrowse, iframe |
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 |
kraken2, qualimap_bamqc, tb_variant_filter, tp_sed_tool, multiqc, bcftools_consensus, mosdepth, tp_awk_tool, __FLATTEN__, fastp, EMBOSS: seqret84, tb_profiler_profile, snippy, tbvcfreport |
Validation, Sequence analysis, Sequencing quality control, Antimicrobial resistance prediction, Taxonomic classification, Variant calling, Global alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment, Sequence alignment, Sequence alignment analysis, Phylogenetic tree generation |
|
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, est_abundance, falco, fastp, recentrifuge |
Sequencing quality control, Taxonomic classification, Read mapping, Sequence contamination filtering, Statistical calculation, Cross-assembly, Expression analysis, Visualisation |
|
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, krakentools_kreport2krona, est_abundance, interactive_tool_pavian, kraken_biom, metaphlan, interactive_tool_phinch, __UNZIP_COLLECTION__, taxonomy_krona_chart |
Genome annotation, Statistical calculation, Aggregation, Taxonomic classification, Visualisation |
|
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, recentrifuge, 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 |
semibin, Fasta_to_Contig2Bin, binette, __BUILD_LIST__, samtools_sort, concoct_extract_fasta_bins, concoct_coverage_table, maxbin2, metabat2_jgi_summarize_bam_contig_depths, concoct_merge_cut_up_clustering, concoct, concoct_cut_up_fasta, metabat2, bowtie2 |
Genome annotation, Read mapping, Read binning, Sequence clustering, Sequence assembly |
|
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 |
, collection_element_identifiers, __FILTER_FROM_FILE__, tp_awk_tool, __FILTER_EMPTY_DATASETS__, mapseq, bedtools_maskfastabed, biom_convert, taxonomy_krona_chart |
Mapping, Visualisation, Formatting, k-mer counting |
|
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 |
collapse_dataset, tp_awk_tool, collection_column_join, ampvis2_load, query_tabular |
Analysis, Visualisation |
|
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 |
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastp, fastqc, mgnify_seqprep, trimmomatic, tp_find_and_replace, __UNZIP_COLLECTION__ |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing, Nucleic acid design |
|
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__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz, fastq_dl |
|
|
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 |
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastqc, trimmomatic, tp_find_and_replace |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing |
|
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 |
, collection_element_identifiers, cshl_fasta_formatter, __FILTER_FROM_FILE__, tp_awk_tool, gops_concat_1, cmsearch_deoverlap, infernal_cmsearch, __FILTER_EMPTY_DATASETS__, mapseq, query_tabular, biom_convert, bedtools_getfastabed, taxonomy_krona_chart |
Mapping, Comparison, Formatting, Alignment, k-mer counting, Nucleic acid feature detection, Visualisation |
|
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 |
Cut1, humann_unpack_pathways, humann_rename_table, humann_split_stratified_table, Grep1, humann_renorm_table, combine_metaphlan2_humann2, tp_find_and_replace, humann_regroup_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 |
dada2_assignTaxonomyAddspecies, dada2_plotQualityProfile, dada2_makeSequenceTable, collection_element_identifiers, dada2_mergePairs, Add_a_column1, phyloseq_from_dada2, tp_replace_in_line, dada2_removeBimeraDenovo, dada2_seqCounts, dada2_filterAndTrim, tp_head_tool, tp_replace_in_column, dada2_learnErrors, __SORTLIST__, dada2_dada, __UNZIP_COLLECTION__, cat1 |
DNA barcoding, Analysis, Deposition, Variant calling, Visualisation |
|
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 |
humann_unpack_pathways, bg_sortmerna, graphlan_annotate, fastqc, export2graphlan, tp_sort_header_tool, Cut1, humann, multiqc, Grep1, combine_metaphlan_humann, tp_find_and_replace, Grouping1, graphlan, humann_renorm_table, humann_regroup_table, taxonomy_krona_chart, cutadapt, fastq_paired_end_interlacer, humann_rename_table, humann_split_stratified_table, metaphlan |
Validation, Species frequency estimation, Sequence composition calculation, Sequence similarity search, Phylogenetic analysis, Sequence alignment analysis, Sequence comparison, Sequencing quality control, Primer removal, Phylogenetic tree editing, Taxonomic classification, Conversion, Phylogenetic tree visualisation, Statistical calculation, Sequence trimming, Read pre-processing, Aggregation, Phylogenetic inference, Visualisation |
|
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 |
Cut1, graphlan_annotate, graphlan, metaphlan, export2graphlan, taxonomy_krona_chart |
Phylogenetic tree editing, Taxonomic classification, Conversion, Phylogenetic tree visualisation, Phylogenetic inference, Visualisation |
|
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, fastq_paired_end_interlacer, bg_sortmerna, fastqc, cutadapt |
Sequence comparison, Validation, Sequencing quality control, Primer removal, Sequence composition calculation, Sequence similarity search, Read pre-processing, Statistical calculation, Sequence trimming, 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 |
humann, humann_unpack_pathways, humann_rename_table, humann_split_stratified_table, Grep1, humann_renorm_table, tp_sort_header_tool, tp_find_and_replace, humann_regroup_table |
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 |
megahit, bandage_info, quast, collection_column_join, bandage_image, coverm_contig, megahit_contig2fastg, metaspades, bowtie2 |
Genome assembly, Sequence assembly visualisation, Local alignment, Read mapping, Sequence assembly validation, 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 |
Count1, fastp, ncbi_blastn_wrapper, cshl_fastq_to_fasta |
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, est_abundance, falco, fastp, recentrifuge |
Sequencing quality control, Taxonomic classification, Read mapping, Sequence contamination filtering, Statistical calculation, Cross-assembly, Expression analysis, Visualisation |
|
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 |
Cut1, Add_a_column1, param_value_from_file, EMBOSS: maskseq51, datamash_ops, Grep1, fasta_compute_length, compose_text_param |
Sequence analysis, Local alignment, Sequence alignment, Sequence alignment analysis, Global 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 |
unicycler, nanoplot, staramr_search, bandage_image, miniasm, PlasFlow, racon, gfa_to_fa, minimap2 |
Mapping assembly, Sequence analysis, Pairwise sequence alignment, Box-Whisker plot plotting, Antimicrobial resistance prediction, De-novo assembly, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, Aggregation |
|
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_count_seqs, mothur_filter_seqs, mothur_classify_otu, mothur_summary_seqs, mothur_pre_cluster, mothur_unique_seqs, mothur_make_shared, mothur_make_biom, mothur_cluster_split, mothur_merge_files, mothur_align_seqs, mothur_make_group, mothur_screen_seqs, mothur_classify_seqs, krona-text |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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, Remove beginning1, multiqc, fastp, fastqc, tp_replace_in_line, porechop, datamash_reverse, taxonomy_krona_chart |
Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence composition calculation, Taxonomic classification, Visualisation |
|
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_renorm_table, humann2_regroup_table, metaphlan2krona, metaphlan2, humann2, taxonomy_krona_chart |
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 |
Cut1, cat1, tp_replace_in_column, Add_a_column1, Filter1, add_column_headers, tp_tail_tool, tp_sorted_uniq, ggplot2_histogram, minimap2, CONVERTER_fasta_to_tabular, MQoutputfilter, histogram_rpy, sort1, count_gff_features, Grouping1, join1, tab2fasta |
Pairwise sequence alignment, Visualisation |
|
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_dist_seqs, mothur_sub_sample, mothur_filter_seqs, mothur_classify_otu, mothur_make_biom, mothur_summary_single, mothur_remove_groups, mothur_dist_shared, mothur_get_groups, mothur_remove_seqs, mothur_count_groups, mothur_taxonomy_to_krona, mothur_make_shared, mothur_cluster_split, mothur_remove_lineage, XY_Plot_1, mothur_classify_seqs, mothur_venn, mothur_summary_seqs, mothur_pre_cluster, mothur_cluster, mothur_make_contigs, taxonomy_krona_chart, mothur_count_seqs, mothur_rarefaction_single, mothur_unique_seqs, mothur_seq_error, mothur_chimera_vsearch, mothur_tree_shared, mothur_align_seqs, mothur_heatmap_sim, mothur_screen_seqs, newick_display |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic analysis, Sequence clustering, Phylogenetic tree reconstruction, Phylogenetic tree generation, Visualisation |
|
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 |
DNA barcoding, Sequence feature detection |
|
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, krakentools_kreport2krona, Filter1, fastp, fastqc, porechop, taxonomy_krona_chart |
Sequence contamination filtering, Statistical calculation, Sequencing quality control, Sequence composition calculation, Aggregation, Taxonomic classification, Visualisation |
|
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_beta_diversity, krakentools_alpha_diversity |
Aggregation, Visualisation |
|
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_remove_lineage, mothur_classify_seqs, mothur_summary_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_count_seqs, mothur_unique_seqs, mothur_screen_seqs, mothur_summary_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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 |
collapse_dataset, newick_display, mothur_tree_shared, mothur_heatmap_sim, mothur_dist_shared, mothur_venn |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic analysis, Sequence clustering, Phylogenetic tree reconstruction, Phylogenetic tree generation, Visualisation |
|
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 |
mothur_rarefaction_single, mothur_summary_single, XY_Plot_1 |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_dist_seqs, mothur_make_shared, mothur_cluster, mothur_rarefaction_single |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_sub_sample, mothur_classify_otu, mothur_count_groups, mothur_make_shared, mothur_cluster_split, mothur_remove_groups |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_remove_seqs, mothur_filter_seqs, mothur_summary_seqs, mothur_pre_cluster, mothur_unique_seqs, mothur_chimera_vsearch, mothur_screen_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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 |
unicycler, nanoplot, staramr_search, bandage_image, miniasm, PlasFlow, racon, gfa_to_fa, minimap2 |
Mapping assembly, Sequence analysis, Pairwise sequence alignment, Box-Whisker plot plotting, Antimicrobial resistance prediction, De-novo assembly, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, Aggregation |
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 |
Sequence contamination filtering, Genome assembly, 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, minimap2, picard_SamToFastq, shovill, ngsutils_bam_filter |
Formatting, Pairwise sequence alignment, Sequencing quality control, Variant calling, Genome assembly, Sequence contamination filtering, Read pre-processing |
|
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 |
kraken2, Kraken2Tax, taxonomy_krona_chart |
Taxonomic classification, Visualisation |
|
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 |
kraken2, Kraken2Tax, taxonomy_krona_chart |
Taxonomic classification, Visualisation |
|
Apache-2.0 |
|
Integrated and Urban Plant Pathology Laboratory |
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 |
kraken2, krakentools_kreport2krona, collection_element_identifiers, est_abundance, Prepare alpha diversity summary file\nPaste1, add_line_to_file, krakentools_alpha_diversity, collection_column_join, __RELABEL_FROM_FILE__, krakentools_beta_diversity, regex1, cat_multiple, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, Fisher results contains a header line we want to exclude "Fisher's alpha...loading"\nShow tail1, Prepare alpha diversity summary file (paste Simpson and Fisher results)\nPaste1, Extract column name and fraction_total_reads from Bracken report\nCut1, krakentools_combine_kreports, taxonomy_krona_chart |
Statistical calculation, Aggregation, Taxonomic classification, Visualisation |
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 |
Cut1, , humann2_renorm_table, humann2_regroup_table, metaphlan2krona, merge_metaphlan_tables, metaphlan2, humann2, taxonomy_krona_chart |
Taxonomic classification, Visualisation |
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 |
mothur_tree_shared, newick_display, mothur_dist_shared, mothur_heatmap_sim |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic analysis, Sequence clustering, Phylogenetic tree reconstruction, Phylogenetic tree generation, Visualisation |
|
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 |
mothur_rarefaction_single, mothur_summary_single, XY_Plot_1 |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_sub_sample, mothur_classify_otu, mothur_count_groups, mothur_make_shared, mothur_cluster_split |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_remove_lineage, mothur_classify_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_count_seqs, mothur_unique_seqs, mothur_screen_seqs, mothur_summary_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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_remove_seqs, mothur_filter_seqs, mothur_summary_seqs, mothur_pre_cluster, mothur_unique_seqs, mothur_chimera_vsearch, mothur_screen_seqs |
DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Phylogenetic analysis, Sequence clustering, Visualisation |
|
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 |
kraken2, qualimap_bamqc, tb_variant_filter, tp_sed_tool, multiqc, bcftools_consensus, mosdepth, tp_awk_tool, __FLATTEN__, fastp, EMBOSS: seqret84, tb_profiler_profile, snippy, tbvcfreport |
Validation, Sequence analysis, Sequencing quality control, Antimicrobial resistance prediction, Taxonomic classification, Variant calling, Global alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment, Sequence alignment, Sequence alignment analysis, Phylogenetic tree generation |
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 |
bbtools_tadpole, srst2, sistr_cmd, seqsero2, mob_recon, kma_map, shovill, hamronize_tool, hamronize_summarize, __UNZIP_COLLECTION__, bbtools_bbduk |
Sequence analysis, Sequence trimming, Genome alignment, Genome indexing, Read mapping, Genome assembly, Clustering, RNA-Seq analysis, Parsing, Antimicrobial resistance prediction, Multilocus sequence typing, Sequence contamination filtering, Data handling, Read binning, Sequence alignment, Visualisation |
|
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 |
collapse_dataset, staramr_search, abricate, tp_find_and_replace, hamronize_tool, hamronize_summarize, shovill |
Data handling, Genome assembly, Parsing, Antimicrobial resistance prediction |
|
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 |
, abricate, cast, Cut1, cat1, datamash_ops, Grep1, tp_text_file_with_recurring_lines, cat_multi_datasets, tp_find_and_replace, hamronize_tool, hamronize_summarize, __MERGE_COLLECTION__, collapse_dataset, staramr_search, tp_split_on_column, addValue, __APPLY_RULES__, shovill |
Data handling, Genome assembly, Parsing, Antimicrobial resistance prediction |
|
MIT |
|
Seq4AMR, ErasmusMC Clinical Bioinformatics |
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, krakentools_kreport2krona, Remove beginning1, sylph_profile, taxpasta, collection_element_identifiers, est_abundance, cat1, add_line_to_file, metaphlan2krona, metaphlan, datamash_transpose, taxonomy_krona_chart |
Formatting, Statistical calculation, Standardisation and normalisation, Aggregation, Taxonomic classification, Conversion, Visualisation |
|
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__, multiqc, collection_element_identifiers, __FLATTEN__, __RELABEL_FROM_FILE__, regex1, checkm2 |
Validation, Statistical calculation, Sequencing quality control, 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 |
|
decontam, Remove beginning1, fastqc, ampvis2_load, ampvis2_export_otu, calculate_numeric_param, multiqc, __FLATTEN__, ampvis2_subset_samples, maaslin2, lotus2, phyloseq_add_rank_names, param_value_from_file, tp_awk_tool, tp_easyjoin_tool, ampvis2_heatmap, biom_convert, compose_text_param, ampvis2_ordinate, bg_column_arrange_by_header, volcanoplot, mmuphin, unzip, phyloseq_from_biom, tp_cut_tool, phyloseq_tax_glom, regex1, datamash_transpose |
DNA barcoding, Validation, Classification, Formatting, Sequencing quality control, Sequence composition calculation, Sequence feature detection, Statistical calculation, Analysis, Filtering, Deposition, Standardisation and normalisation, Visualisation |
|
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, Remove beginning1, humann_unpack_pathways, krakentools_alpha_diversity, csv_to_tabular, sort1, cat1, sylph_profile, humann, collection_element_identifiers, add_line_to_file, tp_text_file_with_recurring_lines, collection_column_join, tp_awk_tool, humann_renorm_table, tp_replace_in_line, tp_easyjoin_tool, humann_regroup_table, taxonomy_krona_chart, krakentools_kreport2krona, taxpasta, collapse_dataset, est_abundance, fastq_paired_end_interlacer, humann_rename_table, metaphlan, tp_sed_tool, datamash_transpose, __UNZIP_COLLECTION__ |
Formatting, Species frequency estimation, Taxonomic classification, Conversion, Statistical calculation, Phylogenetic analysis, Aggregation, Standardisation and normalisation, Visualisation |
|
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 |
|
multiqc, umi_tools_extract, umi_tools_dedup, fastqc, collection_column_join, rna_star, featurecounts, __FILTER_FAILED_DATASETS__ |
Validation, Statistical calculation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Read summarisation, RNA-Seq quantification |
|
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 |
|
hmmer_hmmscan, tp_awk_tool, kofamscan, quast, checkm_lineage_wf, fraggenescan, fastqc, tp_grep_tool, interproscan, sort1, trim_galore, fasplit, coverm_contig, coverm_genome, cat_bins, maxbin2, tp_cat |
Sequence analysis, Multiple sequence alignment, Formatting, Format validation, Validation, Protein feature detection, Sequence composition calculation, Sequence motif recognition, Gene functional annotation, Data retrieval, Sequence database search, Sequence generation, Sequence assembly, Probabilistic sequence generation, Sequencing quality control, Database search, Primer removal, Taxonomic classification, Conversion, Sequence assembly validation, Statistical calculation, Sequence profile generation, Sequence trimming, Local alignment, Read pre-processing, Coding region prediction, Gene prediction, Visualisation |
|
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 |
|
bg_sortmerna, graphlan_annotate, humann2_unpack_pathways, fastqc, export2graphlan, tp_sort_header_tool, format_metaphlan2_output, humann2, multiqc, Grep1, Grouping1, graphlan, metaphlan2krona, metaphlan2, group_humann2_uniref_abundances_to_go, taxonomy_krona_chart, humann2_renorm_table, cutadapt, fastq_paired_end_interlacer, humann2_genefamilies_genus_level, combine_metaphlan2_humann2 |
Sequence comparison, Validation, Formatting, Sequencing quality control, Primer removal, Sequence composition calculation, Phylogenetic tree editing, Taxonomic classification, Sequence similarity search, Conversion, Phylogenetic tree visualisation, Read pre-processing, Statistical calculation, Sequence trimming, Sequence alignment analysis, Phylogenetic inference, Visualisation |
|
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 |
|
bg_sortmerna, kallisto_quant, fastqc, collection_column_join, trim_galore, __UNZIP_COLLECTION__ |
Sequence comparison, Sequencing quality control, Gene expression profiling, Sequence composition calculation, Primer removal, Sequence similarity search, Read pre-processing, Statistical calculation, Sequence trimming, Sequence alignment analysis |
|
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 |
|
Cut1, cat1, gops_intersect_1, collapse_dataset, Add_a_column1, bg_diamond, rbc_mafft, Filter1, tp_split_on_column, regexColumn1, rapidnj, bg_diamond_view, join1, tab2fasta |
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 |
|
unipept, sqlite_to_tabular, search_gui, query_tabular, peptide_shaker |
Prediction and recognition, Visualisation |
|
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 |
|
__EXTRACT_DATASET__, Grep1, map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__ |
|
|
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 |
|
Cut1, Remove beginning1, flashlfq, Filter1, msconvert, tp_replace_in_line, unipept, regex1, search_gui, tp_replace_in_column, query_tabular, peptide_shaker |
Prediction and recognition, Formatting, Filtering, Label-free quantification, Visualisation |
|
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_expand, metaquantome_filter, metaquantome_stat, metaquantome_db, metaquantome_viz |
Indexing, Functional clustering, Statistical inference, Filtering, Differential protein expression analysis, Query and retrieval, Quantification, Heat map generation, Principal component visualisation, Visualisation |
|
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 |
|
kraken2, fastq_to_tabular, seq_filter_by_id, recentrifuge, filter_tabular, 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 |
|
multiqc, bowtie2, featurecounts |
RNA-Seq quantification, Validation, Sequencing quality control, 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 |
Validation, Statistical calculation, Sequencing quality control, 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 |
|
lastz_wrapper_2, tp_grep_tool, tp_sort_header_tool, cat1, Cut1, datamash_ops, Grep1, fasta_filter_by_length, fasta_compute_length, bedtools_intersectbed, bedtools_complementbed, tp_cat, Filter1, mergeCols1, bedtools_sortbed, collapse_dataset, random_lines1, addValue, tp_sed_tool, join1 |
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 |
|
Cut1, cat1, gops_intersect_1, collapse_dataset, Add_a_column1, bg_diamond, rbc_mafft, Filter1, tp_split_on_column, regexColumn1, rapidnj, bg_diamond_view, join1, tab2fasta |
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 |
|
list_organism, create_account, create_or_update, jbrowse, iframe |
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 |
|
bandage_image, gff2bed1, PlasFlow, minimap2, tp_sort_header_tool, deeptools_bam_coverage, circos_wiggle_to_scatter, Cut1, Grep1, circos_gc_skew, tp_text_file_with_recurring_lines, circos, regex_replace, fasta_compute_length, trimmomatic, flye, tp_cat, circos_interval_to_tile, nanoplot, Add_a_column1, tbl2gff3, Filter1, jbrowse, medaka_consensus_pipeline, tp_easyjoin_tool, tp_head_tool, bg_column_arrange_by_header, prokka, staramr_search, ncbi_blastn_wrapper, tp_split_on_column, tp_cut_tool, fasta2tab, regex1, join1, tab2fasta |
Genome annotation, Mapping assembly, Sequence analysis, Coding region prediction, Pairwise sequence alignment, Box-Whisker plot plotting, Sequence visualisation, Base-calling, Gene prediction, Antimicrobial resistance prediction, De-novo assembly, Variant calling, Genome assembly, Sequence assembly visualisation, Scatter plot plotting, Genome visualisation, Cross-assembly, Sequence 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 |
|
tb_variant_filter, bcftools_consensus, snp_dists, snp_sites, tp_cat |
|
|
|
|
|
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 |
|
__MERGE_COLLECTION__, samtools_view, tp_grep_tool, tp_replace_in_line, tb_profiler_profile, addName, tp_sed_tool, tp_cat |
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 |
|
tp_awk_tool, bcftools_view, bcftools_norm, freebayes, vcf2tsv, snpSift_filter, bowtie2 |
Statistical calculation, Read mapping, 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 |
|
collapse_dataset, collection_element_identifiers, bcftools_norm, freebayes, samtools_coverage, samtools_depth, vcf2tsv, tp_cat, bowtie2 |
Statistical calculation, Read mapping, 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 |
|
__MERGE_COLLECTION__, multiqc, collection_element_identifiers, __FLATTEN__, __RELABEL_FROM_FILE__, regex1, checkm2 |
Validation, Statistical calculation, Sequencing quality control, 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__, multiqc, collection_element_identifiers, __FLATTEN__, __RELABEL_FROM_FILE__, regex1, checkm2 |
Validation, Statistical calculation, Sequencing quality control, 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__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz, fastq_dl |
|
|
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 |
|
collection_element_identifiers, __FILTER_FROM_FILE__, tp_awk_tool, __FILTER_EMPTY_DATASETS__, mapseq, bedtools_maskfastabed, biom_convert, taxonomy_krona_chart |
Mapping, Visualisation, Formatting, k-mer counting |
|
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 |
|
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastp, fastqc, mgnify_seqprep, trimmomatic, tp_find_and_replace, __UNZIP_COLLECTION__ |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing, Nucleic acid design |
|
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 |
|
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastqc, trimmomatic, tp_find_and_replace |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing |
|
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 |
|
Cut1, Remove beginning1, collapse_dataset, Count1, bcftools_consensus, snpSift_extractFields, bcftools_norm, tp_cut_tool, CONVERTER_gz_to_uncompressed, table_compute, clair3, regexColumn1, samtools_coverage, minimap2, samtools_depth, tp_head_tool, Paste1, snpSift_filter |
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 |
|
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastqc, trimmomatic, tp_find_and_replace |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing |
|
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 |
|
Cut1, Remove beginning1, collapse_dataset, Count1, bcftools_consensus, snpSift_extractFields, bcftools_norm, tp_cut_tool, CONVERTER_gz_to_uncompressed, table_compute, clair3, regexColumn1, samtools_coverage, minimap2, samtools_depth, tp_head_tool, Paste1, snpSift_filter |
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 |
|
__MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz, fastq_dl |
|
|
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 |
|
collection_element_identifiers, __FILTER_FROM_FILE__, tp_awk_tool, __FILTER_EMPTY_DATASETS__, mapseq, bedtools_maskfastabed, biom_convert, taxonomy_krona_chart |
Mapping, Visualisation, Formatting, k-mer counting |
|
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 |
|
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastp, fastqc, mgnify_seqprep, trimmomatic, tp_find_and_replace, __UNZIP_COLLECTION__ |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing, Nucleic acid design |
|
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 |
|
prinseq, fastq_filter, cshl_fasta_formatter, multiqc, fastq_to_fasta_python, fastqc, trimmomatic, tp_find_and_replace |
Sequence composition calculation, Sequence contamination filtering, Validation, Statistical calculation, Sequencing quality control, Sequence trimming, Read pre-processing |
|
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 |
|
kraken2, Cut1, collapse_dataset, multiqc, nanoplot, Add_a_column1, Grep1, fastp, fastqc, bamtools_split_mapped, collection_column_join, regexColumn1, porechop, krakentools_extract_kraken_reads, minimap2, samtools_fastx, __FILTER_FAILED_DATASETS__ |
Validation, Pairwise sequence alignment, Box-Whisker plot plotting, Sequencing quality control, Sequence composition calculation, Taxonomic classification, Sequence contamination filtering, Data handling, Statistical calculation, Scatter plot plotting, Sequence alignment analysis, Aggregation, Visualisation |
|
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__, multiqc, collection_element_identifiers, __FLATTEN__, __RELABEL_FROM_FILE__, regex1, checkm2 |
Validation, Statistical calculation, Sequencing quality control, 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 |
|
Cut1, Remove beginning1, collapse_dataset, Count1, bcftools_consensus, snpSift_extractFields, bcftools_norm, tp_cut_tool, CONVERTER_gz_to_uncompressed, table_compute, clair3, regexColumn1, samtools_coverage, minimap2, samtools_depth, tp_head_tool, Paste1, snpSift_filter |
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 |
|
Cut1, Remove beginning1, collapse_dataset, Count1, bcftools_consensus, snpSift_extractFields, bcftools_norm, tp_cut_tool, CONVERTER_gz_to_uncompressed, table_compute, clair3, regexColumn1, samtools_coverage, minimap2, samtools_depth, tp_head_tool, Paste1, snpSift_filter |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |