|
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, __UNZIP_COLLECTION__, collection_element_identifiers, fastq_paired_end_interlacer, argnorm, multiqc, Remove a collection level so that outputs can be taken into account by tooldistillator\n__FLATTEN__, tp_text_file_with_recurring_lines, Removal of the first argNorm line that causes a multiQC error\nRemove beginning1, table_pandas_rename_column, tooldistillator, Removal of the first line because it is not necessary for tooldistillator\nRemove beginning1, deeparg_short_reads, __FILTER_FAILED_DATASETS__, groot, tooldistillator_summarize, __RELABEL_FROM_FILE__ |
Sequencing quality control, Data parsing, Taxonomic classification, Validation, Gene functional annotation, Antimicrobial resistance prediction |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
cgmlst-bacterial-genome/main |
WorkflowHub |
2055 |
https://workflowhub.eu/workflows/2055?version=1 |
ABRomics None, Clea Siguret, Hugo Lefeuvre |
|
2026-01-21 |
2026-01-25 |
1 |
1 |
3.0 |
coreprofiler_allele_calling, tooldistillator, tooldistillator_summarize |
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 |
pick_value, tooldistillator_summarize, collapse_dataset, quast, kraken2, tooldistillator, recentrifuge, est_abundance, checkm2 |
Sequencing quality control, Cross-assembly, Expression analysis, Data parsing, Validation, Statistical calculation, Sequence assembly validation, Taxonomic classification, Visualisation, Sequence composition calculation |
|
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 |
pangolin, ivar_trim, samtools_stats, multiqc, fastp, ivar_variants, __FLATTEN__, tp_cat, tp_sed_tool, nextclade, qualimap_bamqc, snpeff_sars_cov_2, ivar_consensus, samtools_view, bwa_mem |
Sequencing quality control, Read mapping, Primer removal, Validation, Variant classification, Sequence contamination filtering, Methylation analysis, Genome indexing, SNP detection, Generation, Variant calling, Tree-based sequence alignment, 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 |
multiqc, samtools_stats, lofreq_indelqual, lofreq_filter, fastp, picard_MarkDuplicates, snpeff_sars_cov_2, samtools_view, lofreq_viterbi, lofreq_call, bwa_mem |
Sequencing quality control, Read mapping, Validation, Formatting, Sequence contamination filtering, Genome indexing, Generation, SNP detection, 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 |
snpEff, pick_value, multiqc, samtools_stats, collapse_dataset, snpEff_build_gb, __FLATTEN__, lofreq_viterbi, qualimap_bamqc, map_param_value, __FILTER_FAILED_DATASETS__, ivar_consensus, samtools_view, fastp, tp_sed_tool, calculate_numeric_param, tp_find_and_replace, ivar_trim, tp_cat, snpSift_extractFields, ivar_variants, bwa_mem |
Sequencing quality control, Sequence contamination filtering, Genome indexing, Read mapping, Primer removal, Generation, Validation, 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 |
__UNZIP_COLLECTION__, __HARMONIZELISTS__, collection_element_identifiers, Cut1, collapse_dataset, __FLATTEN__, wc_gnu, 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__, param_value_from_file, qualimap_bamqc, tp_text_file_with_recurring_lines, iqtree, tp_easyjoin_tool, __FILTER_FAILED_DATASETS__, ivar_consensus, samtools_view, __APPLY_RULES__, rbc_mafft, fastp, __FILTER_FROM_FILE__, tp_find_and_replace, bamtools_split_ref, vapor, seqtk_subseq, This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment).\n__APPLY_RULES__, __MERGE_COLLECTION__, Grep1, tp_cat, Filter1, Paste1, Show beginning1, snipit, __DUPLICATE_FILE_TO_COLLECTION__, __RELABEL_FROM_FILE__, bwa_mem |
Sequencing quality control, Phylogenetic analysis, Data handling, Read mapping, Primer removal, Base position variability plotting, Sequence file editing, Multiple sequence alignment, Sequence analysis, Data retrieval, Sequence contamination filtering, Genome indexing, Generation, De-novo assembly, Sequence alignment analysis, Sequence alignment |
|
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 |
collection_element_identifiers, Cut1, samtools_stats, multiqc, samtools_merge, __FLATTEN__, compose_text_param, qualimap_bamqc, param_value_from_file, fasta_compute_length, __FILTER_FAILED_DATASETS__, datamash_ops, ivar_consensus, samtools_view, __SORTLIST__, __APPLY_RULES__, __ZIP_COLLECTION__, fastp, split_file_to_collection, EMBOSS: maskseq51, tp_sed_tool, ivar_trim, Grep1, tp_cat, bwa_mem |
Sequencing quality control, Read mapping, Primer removal, Local alignment, Validation, Sequence analysis, Sequence contamination filtering, Global alignment, Genome indexing, Generation, Sequence alignment analysis, Sequence 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 |
snpSift_filter, table_compute, Cut1, collapse_dataset, minimap2, Remove beginning1, CONVERTER_gz_to_uncompressed, Paste1, regexColumn1, clair3, tp_cut_tool, bcftools_consensus, snpSift_extractFields, Count1, samtools_coverage, bcftools_norm, samtools_depth, tp_head_tool |
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 |
, fastq_dl, __MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz |
|
|
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, bedtools_maskfastabed, mapseq, taxonomy_krona_chart, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, biom_convert |
k-mer counting, Mapping, Formatting, Visualisation |
|
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, __UNZIP_COLLECTION__, fastq_filter, multiqc, fastqc, fastp, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace, mgnify_seqprep |
Sequencing quality control, Validation, Nucleic acid design, Statistical calculation, Sequence contamination filtering, Sequence trimming, Read pre-processing, 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 |
prinseq, fastq_filter, multiqc, fastqc, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace |
Sequence contamination filtering, Sequencing quality control, Sequence composition calculation, Sequence trimming, Validation, Read pre-processing, Statistical calculation |
|
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, , collection_element_identifiers, mapseq, taxonomy_krona_chart, gops_concat_1, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, query_tabular, biom_convert, infernal_cmsearch, cmsearch_deoverlap, cshl_fasta_formatter |
k-mer counting, Comparison, Nucleic acid feature detection, Mapping, Alignment, Formatting, 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, query_tabular, collection_column_join, Grouping1, filter_tabular |
|
|
MIT |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
clinicalmp-discovery/main |
WorkflowHub |
1225 |
https://workflowhub.eu/workflows/1225?version=1 |
Subina Mehta |
|
2024-12-10 |
2025-11-27 |
1 |
1 |
24.0 |
msconvert, Cut1, dbbuilder, Remove beginning1, fasta_merge_files_and_filter_unique_sequences, fasta_cli, Grep1, Filter1, query_tabular, tp_cat, search_gui, fasta2tab, ident_params, Grouping1, filter_tabular, peptide_shaker, maxquant |
Principal component plotting, Protein quantification, Heat map generation, Formatting, Statistical calculation, Filtering, Clustering, Standardisation and normalisation, Imputation, 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, msstatstmt, Grep1 |
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 |
Cut1, dbbuilder, uniprotxml_downloader, collapse_dataset, Remove beginning1, fasta_merge_files_and_filter_unique_sequences, query_tabular, tp_cat, Filter1, pepquery2, Grouping1 |
|
|
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, de Novo sequencing, Target-Decoy, 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 |
Quantified-Peptides\nGrouping1, extract proteins\nCut1, extract peptides\nCut1, extracting microbial Proteins\nGrep1, Quantified-Proteins\nGrouping1, extracting microbial Peptides\nGrep1, maxquant |
Principal component plotting, Protein quantification, Heat map generation, Statistical calculation, Clustering, Standardisation and normalisation, Imputation, 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_image, tooldistillator, shovill, bandage_info, tooldistillator_summarize |
Genome assembly, Sequence assembly visualisation, Data parsing |
|
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 |
__UNZIP_COLLECTION__, __ZIP_COLLECTION__, fastp, tooldistillator_summarize, kraken2, tooldistillator, recentrifuge, est_abundance |
Sequencing quality control, Sequence contamination filtering, Cross-assembly, Expression analysis, Data parsing, Taxonomic classification, Statistical calculation |
|
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 |
Phylogenetic tree for diversity analysis, Rarefaction, 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 |
collection_element_identifiers, medaka_consensus_pipeline, __BUILD_LIST__, bandage_image, abricate, tab2fasta, split_file_to_collection, flye, fasta2tab, compose_text_param, tp_find_and_replace, param_value_from_file |
Mapping assembly, Cross-assembly, Antimicrobial resistance prediction, Genome assembly, Base-calling, Variant calling, Sequence assembly, Sequence assembly visualisation, De-novo assembly |
|
MIT |
10.48546/workflowhub.workflow.1062.1 |
Intergalactic Workflow Commission (IWC) |
True |
False |
|
pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main |
WorkflowHub |
1060 |
https://workflowhub.eu/workflows/1060?version=1 |
Engy Nasr, Bérénice Batut, Paul Zierep |
|
2024-06-26 |
2025-11-27 |
1 |
1 |
60.0 |
Cut1, collapse_dataset, regex1, __FILTER_EMPTY_DATASETS__, fasta_merge_files_and_filter_unique_sequences, collection_column_join, bedtools_getfastabed, ggplot2_heatmap, tp_sorted_uniq, Remove beginning1, tp_split_on_column, regexColumn1, __FILTER_FAILED_DATASETS__, clustalw, Grouping1, tab2fasta, newick_display, fasta2tab, tp_multijoin_tool, Count1, fasttree, tp_replace_in_column |
Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis, Phylogenetic tree reconstruction, Multiple sequence alignment, Mapping, 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 |
taxonomy_krona_chart, kraken2, krakentools_kreport2krona |
Taxonomic classification, Visualisation, 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 |
bakta, plasmidfinder, isescan, tooldistillator, tooldistillator_summarize, integron_finder |
Protein feature detection, Genome annotation, Data parsing, Scaffolding, Multilocus sequence typing, Genome assembly, Nucleic acid feature detection, Sequence motif recognition, Structural variation detection |
|
GPL-3.0-or-later |
|
Intergalactic Workflow Commission (IWC) |
True |
False |
|
amr_gene_detection/main |
WorkflowHub |
1049 |
https://workflowhub.eu/workflows/1049?version=9 |
ABRomics None, Pierre Marin, Clea Siguret |
abromics, amr, amr-detection, genomics, antibiotic-resistance, antimicrobial resistance, antimicrobial-resistance-genes, bacterial-genomics, fasta |
2025-12-04 |
2025-12-04 |
9 |
9 |
5.0 |
abricate, tooldistillator, tooldistillator_summarize, amrfinderplus, staramr_search |
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, __UNZIP_COLLECTION__, __APPLY_RULES__, dada2_plotQualityProfile, dada2_makeSequenceTable, dada2_learnErrors, dada2_dada, dada2_mergePairs, dada2_assignTaxonomyAddspecies, dada2_seqCounts, dada2_removeBimeraDenovo |
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, jbrowse, iframe, create_or_update |
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 |
mosdepth, multiqc, tb_profiler_profile, fastp, snippy, kraken2, __FLATTEN__, tp_awk_tool, tp_sed_tool, bcftools_consensus, EMBOSS: seqret84, tbvcfreport, tb_variant_filter, qualimap_bamqc |
Sequencing quality control, Local alignment, Phylogenetic tree generation, Validation, Sequence analysis, Antimicrobial resistance prediction, Sequence contamination filtering, Global alignment, Variant calling, Taxonomic classification, Sequence alignment analysis, Sequence alignment, Phylogenetic tree visualisation |
|
AGPL-3.0-or-later |
|
Galaxy Training Network |
True |
False |
|
Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
WorkflowHub |
2043 |
https://workflowhub.eu/workflows/2043?version=1 |
|
gtn, galaxy, sequence-analysis |
2025-12-22 |
2025-12-22 |
1 |
1 |
5.0 |
falco, fastp, kraken2, recentrifuge, est_abundance |
Sequencing quality control, Read mapping, Sequence contamination filtering, Cross-assembly, Expression analysis, Taxonomic classification, Visualisation, Statistical calculation |
|
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 |
metaphlan, __UNZIP_COLLECTION__, krakentools_kreport2krona, taxonomy_krona_chart, kraken2, interactive_tool_phinch, interactive_tool_pavian, est_abundance, kraken_biom |
Genome annotation, Taxonomic classification, Visualisation, Aggregation, Statistical calculation |
|
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 |
est_abundance, kraken2, recentrifuge |
Cross-assembly, Expression analysis, Taxonomic classification, Statistical calculation |
|
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 |
Fasta_to_Contig2Bin, metabat2, concoct, __BUILD_LIST__, metabat2_jgi_summarize_bam_contig_depths, binette, concoct_coverage_table, maxbin2, concoct_merge_cut_up_clustering, semibin, bowtie2, samtools_sort, concoct_extract_fasta_bins, concoct_cut_up_fasta |
Read mapping, Genome annotation, Sequence clustering, Read binning, 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, bedtools_maskfastabed, mapseq, taxonomy_krona_chart, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, biom_convert |
k-mer counting, Mapping, Formatting, Visualisation |
|
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, ampvis2_load, tp_awk_tool, query_tabular, collection_column_join |
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 |
prinseq, __UNZIP_COLLECTION__, fastq_filter, multiqc, fastqc, fastp, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace, mgnify_seqprep |
Sequencing quality control, Validation, Nucleic acid design, Statistical calculation, Sequence contamination filtering, Sequence trimming, Read pre-processing, 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 |
, fastq_dl, __MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz |
|
|
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, query_tabular, collection_column_join, Grouping1, filter_tabular |
|
|
MIT |
|
Galaxy Training Network |
True |
False |
|
MGnify's amplicon pipeline v5.0 - Quality control SE |
WorkflowHub |
1850 |
https://workflowhub.eu/workflows/1850?version=1 |
|
amplicon, gtn, galaxy, metagenomics, mgnify_amplicon, name:microgalaxy |
2025-08-11 |
2025-08-11 |
1 |
1 |
14.0 |
prinseq, fastq_filter, multiqc, fastqc, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace |
Sequence contamination filtering, Sequencing quality control, Sequence composition calculation, Sequence trimming, Validation, Read pre-processing, Statistical calculation |
|
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, , collection_element_identifiers, mapseq, taxonomy_krona_chart, gops_concat_1, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, query_tabular, biom_convert, infernal_cmsearch, cmsearch_deoverlap, cshl_fasta_formatter |
k-mer counting, Comparison, Nucleic acid feature detection, Mapping, Alignment, Formatting, 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 |
humann_regroup_table, Cut1, humann_unpack_pathways, humann_renorm_table, humann_split_stratified_table, Grep1, humann_rename_table, combine_metaphlan2_humann2, tp_find_and_replace |
Phylogenetic analysis, Taxonomic classification, Species frequency estimation |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Building an amplicon sequence variant (ASV) table from 16S data using DADA2 |
WorkflowHub |
1395 |
https://workflowhub.eu/workflows/1395?version=2 |
|
gtn, galaxy, microbiome |
2025-07-07 |
2025-07-07 |
2 |
2 |
21.0 |
dada2_filterAndTrim, __UNZIP_COLLECTION__, __SORTLIST__, collection_element_identifiers, tp_replace_in_line, dada2_plotQualityProfile, Add_a_column1, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_learnErrors, dada2_dada, cat1, dada2_mergePairs, dada2_assignTaxonomyAddspecies, dada2_seqCounts, dada2_removeBimeraDenovo, tp_head_tool, tp_replace_in_column |
Deposition, Analysis, Variant calling, Visualisation, DNA barcoding |
|
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 |
graphlan_annotate, multiqc, Cut1, export2graphlan, humann_rename_table, tp_sort_header_tool, metaphlan, bg_sortmerna, Grouping1, combine_metaphlan_humann, humann, humann_regroup_table, fastq_paired_end_interlacer, fastqc, humann_unpack_pathways, tp_find_and_replace, taxonomy_krona_chart, humann_renorm_table, humann_split_stratified_table, Grep1, cutadapt, graphlan |
Phylogenetic tree editing, Sequence comparison, Taxonomic classification, Sequence alignment analysis, Sequence trimming, Sequence similarity search, Species frequency estimation, Sequencing quality control, Phylogenetic analysis, Primer removal, Conversion, Validation, Aggregation, Statistical calculation, Phylogenetic tree visualisation, Phylogenetic inference, Visualisation, Read pre-processing, Sequence composition calculation |
|
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_annotate, metaphlan, taxonomy_krona_chart, Cut1, export2graphlan, graphlan |
Conversion, Phylogenetic inference, Phylogenetic tree editing, Phylogenetic tree visualisation, Taxonomic classification, 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, fastqc, bg_sortmerna, cutadapt |
Sequencing quality control, Primer removal, Validation, Statistical calculation, Sequence comparison, Sequence alignment analysis, Sequence trimming, Read pre-processing, Sequence similarity search, Sequence composition calculation |
|
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, humann_regroup_table, humann_unpack_pathways, humann_renorm_table, humann_split_stratified_table, Grep1, humann_rename_table, tp_find_and_replace, humann |
Phylogenetic analysis, Taxonomic classification, Species frequency estimation |
|
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_contig2fastg, bandage_image, quast, metaspades, megahit, collection_column_join, bandage_info, bowtie2, coverm_contig |
Read mapping, Genome assembly, Sequence assembly validation, Local alignment, Visualisation, 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 |
fastp, cshl_fastq_to_fasta, Count1, ncbi_blastn_wrapper |
Sequencing quality control, Sequence contamination filtering |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
WorkflowHub |
1644 |
https://workflowhub.eu/workflows/1644?version=1 |
|
gtn, galaxy, sequence-analysis |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
falco, fastp, kraken2, recentrifuge, est_abundance |
Sequencing quality control, Read mapping, Sequence contamination filtering, Cross-assembly, Expression analysis, Taxonomic classification, Visualisation, Statistical calculation |
|
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, fasta_compute_length, Grep1, EMBOSS: maskseq51, compose_text_param, datamash_ops, param_value_from_file |
Global alignment, Sequence alignment, Local alignment, Sequence alignment analysis, Sequence analysis |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Copy Of GTN Training - Antibiotic Resistance Detection |
WorkflowHub |
1477 |
https://workflowhub.eu/workflows/1477?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
12.0 |
bandage_image, nanoplot, minimap2, miniasm, PlasFlow, gfa_to_fa, staramr_search, unicycler, racon |
Mapping assembly, Box-Whisker plot plotting, Aggregation, Sequence analysis, Antimicrobial resistance prediction, Scatter plot plotting, Genome assembly, Pairwise sequence alignment, De-novo assembly, Sequence assembly visualisation |
|
CC-BY-4.0 |
|
Galaxy Training Network |
True |
False |
|
Amplicon Tutorial |
WorkflowHub |
1476 |
https://workflowhub.eu/workflows/1476?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
17.0 |
mothur_pre_cluster, mothur_align_seqs, mothur_merge_files, mothur_make_biom, mothur_make_shared, mothur_classify_seqs, mothur_screen_seqs, mothur_classify_otu, mothur_filter_seqs, krona-text, mothur_summary_seqs, mothur_count_seqs, mothur_make_group, mothur_cluster_split, mothur_unique_seqs |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
tp_replace_in_line, multiqc, fastqc, taxonomy_krona_chart, fastp, kraken2, Remove beginning1, datamash_reverse, porechop |
Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification, Visualisation, Validation, Statistical calculation |
|
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, taxonomy_krona_chart, metaphlan2krona, humann2, metaphlan2, humann2_regroup_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_sorted_uniq, Cut1, Add_a_column1, histogram_rpy, sort1, minimap2, tab2fasta, MQoutputfilter, ggplot2_histogram, Filter1, cat1, count_gff_features, Grouping1, CONVERTER_fasta_to_tabular, add_column_headers, join1, tp_replace_in_column |
Visualisation, Pairwise sequence alignment |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Training: 16S rRNA Sequencing With Mothur: Main Tutorial |
WorkflowHub |
1465 |
https://workflowhub.eu/workflows/1465?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
38.0 |
mothur_pre_cluster, mothur_taxonomy_to_krona, mothur_dist_seqs, mothur_screen_seqs, mothur_filter_seqs, mothur_seq_error, mothur_tree_shared, mothur_count_seqs, mothur_rarefaction_single, mothur_unique_seqs, mothur_cluster, mothur_remove_lineage, mothur_count_groups, XY_Plot_1, mothur_classify_seqs, mothur_make_contigs, mothur_chimera_vsearch, mothur_get_groups, mothur_summary_single, mothur_remove_groups, mothur_make_shared, mothur_classify_otu, mothur_dist_shared, newick_display, mothur_remove_seqs, mothur_sub_sample, mothur_venn, mothur_align_seqs, mothur_make_biom, taxonomy_krona_chart, mothur_heatmap_sim, mothur_cluster_split, mothur_summary_seqs |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
krakentools_kreport2krona, fastqc, taxonomy_krona_chart, fastp, kraken2, Filter1, porechop |
Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification, Visualisation, Aggregation, Statistical calculation |
|
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_classify_seqs, mothur_remove_lineage, mothur_summary_seqs |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1418 |
https://workflowhub.eu/workflows/1418?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
mothur_venn, collapse_dataset, mothur_heatmap_sim, mothur_dist_shared, newick_display, mothur_tree_shared |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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_dist_seqs, mothur_rarefaction_single, mothur_make_shared |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1404 |
https://workflowhub.eu/workflows/1404?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
6.0 |
mothur_remove_groups, mothur_count_groups, mothur_make_shared, mothur_classify_otu, mothur_cluster_split, mothur_sub_sample |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
MIT |
|
Galaxy Training Network |
True |
False |
|
Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] |
WorkflowHub |
1400 |
https://workflowhub.eu/workflows/1400?version=1 |
|
gtn, galaxy, microbiome |
2025-06-02 |
2025-06-02 |
1 |
1 |
9.0 |
mothur_pre_cluster, mothur_screen_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_summary_seqs, mothur_remove_seqs, mothur_unique_seqs |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
bandage_image, nanoplot, minimap2, miniasm, PlasFlow, gfa_to_fa, staramr_search, unicycler, racon |
Mapping assembly, Box-Whisker plot plotting, Aggregation, Sequence analysis, Antimicrobial resistance prediction, Scatter plot plotting, Genome assembly, Pairwise sequence alignment, De-novo assembly, Sequence assembly visualisation |
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 |
Sequencing quality control, Genome assembly, Sequence contamination filtering |
|
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 |
samtools_stats, ngsutils_bam_filter, minimap2, fasta_merge_files_and_filter_unique_sequences, shovill, picard_SamToFastq, ncbi_blastn_wrapper |
Sequencing quality control, Sequence contamination filtering, Genome assembly, Pairwise sequence alignment, Variant calling, Read pre-processing, 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 |
Kraken2Tax, taxonomy_krona_chart, kraken2 |
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 |
Kraken2Tax, taxonomy_krona_chart, kraken2 |
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 |
krakentools_kreport2krona, taxonomy_krona_chart, collection_element_identifiers, Prepare alpha diversity summary file\nPaste1, krakentools_combine_kreports, krakentools_beta_diversity, kraken2, Extract column name and fraction_total_reads from Bracken report\nCut1, Prepare alpha diversity summary file (paste sample identifiers and Simpson results)\nPaste1, krakentools_alpha_diversity, collection_column_join, 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, est_abundance, regex1, cat_multiple, __RELABEL_FROM_FILE__, add_line_to_file |
Taxonomic classification, Visualisation, Aggregation, Statistical calculation |
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 |
, taxonomy_krona_chart, Cut1, humann2_renorm_table, metaphlan2krona, humann2, merge_metaphlan_tables, metaphlan2, humann2_regroup_table |
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 |
newick_display, mothur_tree_shared, mothur_heatmap_sim, mothur_dist_shared |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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_count_groups, mothur_make_shared, mothur_classify_otu, mothur_cluster_split, mothur_sub_sample |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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_pre_cluster, mothur_screen_seqs, mothur_chimera_vsearch, mothur_filter_seqs, mothur_summary_seqs, mothur_remove_seqs, mothur_unique_seqs |
Sequencing quality control, Phylogenetic analysis, Sequence clustering, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding |
|
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 |
mosdepth, multiqc, tb_profiler_profile, fastp, snippy, kraken2, __FLATTEN__, tp_awk_tool, tp_sed_tool, bcftools_consensus, EMBOSS: seqret84, tbvcfreport, tb_variant_filter, qualimap_bamqc |
Sequencing quality control, Local alignment, Phylogenetic tree generation, Validation, Sequence analysis, Antimicrobial resistance prediction, Sequence contamination filtering, Global alignment, Variant calling, Taxonomic classification, Sequence alignment analysis, Sequence alignment, Phylogenetic tree visualisation |
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 |
__UNZIP_COLLECTION__, sistr_cmd, seqsero2, kma_map, bbtools_bbduk, hamronize_summarize, mob_recon, shovill, hamronize_tool, bbtools_tadpole, srst2 |
Read mapping, Data handling, Sequence analysis, Genome indexing, Sequence contamination filtering, RNA-Seq analysis, Read binning, Genome alignment, Sequence trimming, Antimicrobial resistance prediction, Multilocus sequence typing, Visualisation, Genome assembly, Clustering, Parsing, Sequence alignment |
|
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 |
abricate, collapse_dataset, hamronize_summarize, shovill, staramr_search, hamronize_tool, tp_find_and_replace |
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 |
, Cut1, abricate, collapse_dataset, cast, hamronize_tool, tp_text_file_with_recurring_lines, hamronize_summarize, tp_split_on_column, datamash_ops, __APPLY_RULES__, shovill, tp_find_and_replace, addValue, __MERGE_COLLECTION__, Grep1, cat_multi_datasets, cat1, staramr_search |
Data handling, Genome assembly, Parsing, Antimicrobial resistance prediction |
|
MIT |
|
Seq4AMR, ErasmusMC Clinical Bioinformatics |
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 |
|
cat_bins, trim_galore, checkm_lineage_wf, fasplit, fastqc, tp_grep_tool, sort1, quast, tp_awk_tool, tp_cat, hmmer_hmmscan, maxbin2, fraggenescan, interproscan, coverm_genome, coverm_contig |
Sequence generation, Local alignment, Multiple sequence alignment, Data retrieval, Coding region prediction, Sequence database search, Taxonomic classification, Sequence profile generation, Sequence trimming, Sequence assembly, Sequencing quality control, Protein feature detection, Format validation, Primer removal, Gene prediction, Conversion, Validation, Database search, Formatting, Statistical calculation, Probabilistic sequence generation, Sequence assembly validation, Visualisation, Sequence motif recognition, Read pre-processing, Sequence composition calculation |
|
|
|
|
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 |
|
sylph_profile, metaphlan, collection_element_identifiers, taxonomy_krona_chart, krakentools_kreport2krona, metaphlan2krona, kraken2, Remove beginning1, datamash_transpose, cat1, taxpasta, est_abundance, add_line_to_file |
Conversion, Standardisation and normalisation, Taxonomic classification, Visualisation, Aggregation, Formatting, Statistical calculation |
|
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 |
|
collection_element_identifiers, multiqc, __MERGE_COLLECTION__, __FLATTEN__, checkm2, regex1, __RELABEL_FROM_FILE__ |
Sequencing quality control, Sequence assembly validation, Sequence composition calculation, Validation, Statistical calculation |
|
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 |
|
multiqc, __FLATTEN__, compose_text_param, ampvis2_ordinate, param_value_from_file, Remove beginning1, decontam, tp_easyjoin_tool, volcanoplot, phyloseq_add_rank_names, fastqc, unzip, maaslin2, lotus2, phyloseq_tax_glom, tp_awk_tool, datamash_transpose, ampvis2_load, ampvis2_heatmap, calculate_numeric_param, ampvis2_subset_samples, phyloseq_from_biom, ampvis2_export_otu, bg_column_arrange_by_header, biom_convert, tp_cut_tool, mmuphin, regex1 |
Sequencing quality control, Deposition, Sequence feature detection, Classification, Validation, Formatting, Statistical calculation, Filtering, Standardisation and normalisation, DNA barcoding, Visualisation, Analysis, Sequence composition calculation |
|
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 |
|
__UNZIP_COLLECTION__, collection_element_identifiers, sort1, collapse_dataset, humann_rename_table, collection_column_join, metaphlan, tp_text_file_with_recurring_lines, Remove beginning1, tp_easyjoin_tool, est_abundance, humann, humann_regroup_table, fastq_paired_end_interlacer, humann_unpack_pathways, tp_awk_tool, datamash_transpose, tp_sed_tool, sylph_profile, tp_replace_in_line, taxonomy_krona_chart, krakentools_kreport2krona, humann_renorm_table, kraken2, krakentools_alpha_diversity, cat1, taxpasta, csv_to_tabular, add_line_to_file |
Phylogenetic analysis, Conversion, Aggregation, Formatting, Statistical calculation, Standardisation and normalisation, Taxonomic classification, Visualisation, Species frequency estimation |
|
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, fastqc, umi_tools_extract, featurecounts, umi_tools_dedup, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star |
Sequencing quality control, RNA-Seq quantification, Sequence composition calculation, Read summarisation, Validation, Sequence alignment, Statistical calculation |
|
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 |
|
cat_bins, trim_galore, checkm_lineage_wf, fasplit, fastqc, tp_grep_tool, kofamscan, sort1, quast, tp_awk_tool, tp_cat, hmmer_hmmscan, maxbin2, fraggenescan, interproscan, coverm_genome, coverm_contig |
Sequence generation, Local alignment, Multiple sequence alignment, Sequence analysis, Data retrieval, Coding region prediction, Sequence database search, Taxonomic classification, Sequence profile generation, Sequence trimming, Sequence assembly, Gene functional annotation, Sequencing quality control, Protein feature detection, Format validation, Primer removal, Gene prediction, Conversion, Validation, Database search, Formatting, Statistical calculation, Probabilistic sequence generation, Sequence assembly validation, Visualisation, Sequence motif recognition, Read pre-processing, Sequence composition calculation |
|
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 |
|
graphlan_annotate, multiqc, export2graphlan, humann2_genefamilies_genus_level, tp_sort_header_tool, humann2_unpack_pathways, bg_sortmerna, Grouping1, fastq_paired_end_interlacer, fastqc, graphlan, format_metaphlan2_output, group_humann2_uniref_abundances_to_go, humann2_renorm_table, taxonomy_krona_chart, humann2, metaphlan2krona, metaphlan2, Grep1, cutadapt, combine_metaphlan2_humann2 |
Sequencing quality control, Primer removal, Conversion, Phylogenetic inference, Validation, Phylogenetic tree editing, Formatting, Statistical calculation, Sequence comparison, Phylogenetic tree visualisation, Taxonomic classification, Visualisation, Sequence alignment analysis, Sequence trimming, Read pre-processing, Sequence similarity search, Sequence composition calculation |
|
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, __UNZIP_COLLECTION__, fastqc, bg_sortmerna, collection_column_join, kallisto_quant |
Sequencing quality control, Primer removal, Sequence alignment analysis, Statistical calculation, Sequence comparison, Sequence trimming, Read pre-processing, Sequence similarity search, Gene expression profiling, Sequence composition calculation |
|
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 |
|
rapidnj, rbc_mafft, Cut1, Add_a_column1, collapse_dataset, bg_diamond_view, tab2fasta, tp_split_on_column, Filter1, cat1, regexColumn1, bg_diamond, gops_intersect_1, join1 |
Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis |
|
|
|
|
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, query_tabular, search_gui, peptide_shaker |
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 |
|
__BUILD_LIST__, __FILTER_EMPTY_DATASETS__, Grep1, map_param_value, __EXTRACT_DATASET__ |
|
|
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 |
|
msconvert, unipept, tp_replace_in_line, Cut1, Remove beginning1, query_tabular, Filter1, search_gui, flashlfq, peptide_shaker, regex1, tp_replace_in_column |
Filtering, Formatting, Label-free quantification, Visualisation, Prediction and recognition |
|
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_stat, metaquantome_filter, metaquantome_db, metaquantome_viz |
Statistical inference, Heat map generation, Query and retrieval, Quantification, Principal component visualisation, Filtering, Indexing, Visualisation, Functional clustering, Differential protein expression analysis |
|
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 |
|
seq_filter_by_id, kraken2, fastq_to_tabular, recentrifuge, bowtie2, filter_tabular |
Taxonomic classification, Read mapping, Cross-assembly, Expression analysis |
|
MIT |
|
|
True |
False |
|
Cloud-Aerosole MT-MG Functional Profiling |
https://usegalaxy.eu |
63478edcea3f449a |
https://usegalaxy.eu/published/workflow?id=63478edcea3f449a |
Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato |
metagenomics, metatranscriptomics, name:microgalaxy |
2024-11-21 |
2024-11-21 |
4 |
4 |
|
bowtie2, multiqc, featurecounts |
Read mapping, Sequencing quality control, RNA-Seq quantification, Read summarisation, Validation |
|
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 |
|
multiqc, fastqc, trimmomatic |
Sequencing quality control, Sequence composition calculation, Validation, Statistical 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 |
|
interactive_tool_jupyter_notebook, __BUILD_LIST__ |
|
|
|
|
|
True |
False |
|
Ecoli Comparison |
https://usegalaxy.eu |
0e492839192d26e0 |
https://usegalaxy.eu/published/workflow?id=0e492839192d26e0 |
|
assembly, name:microgalaxy |
2023-12-14 |
2023-12-14 |
0 |
0 |
|
tp_grep_tool, Cut1, bedtools_intersectbed, collapse_dataset, bedtools_sortbed, join1, tp_sort_header_tool, bedtools_complementbed, fasta_filter_by_length, fasta_compute_length, mergeCols1, datamash_ops, random_lines1, tp_sed_tool, addValue, lastz_wrapper_2, Grep1, Filter1, tp_cat, cat1 |
Read mapping, Mapping, Sequence alignment |
|
|
|
|
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 |
|
rapidnj, rbc_mafft, Cut1, Add_a_column1, collapse_dataset, bg_diamond_view, tab2fasta, tp_split_on_column, Filter1, cat1, regexColumn1, bg_diamond, gops_intersect_1, join1 |
Multiple sequence alignment, Phylogenetic tree generation, Sequence alignment analysis |
|
|
|
|
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, jbrowse, iframe, create_or_update |
Genome visualisation |
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|
|
|
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 |
|
medaka_consensus_pipeline, Cut1, Add_a_column1, minimap2, circos_wiggle_to_scatter, circos_interval_to_tile, tp_head_tool, join1, tp_sort_header_tool, circos, jbrowse, tbl2gff3, regex_replace, tp_text_file_with_recurring_lines, fasta_compute_length, tp_split_on_column, trimmomatic, tp_easyjoin_tool, prokka, circos_gc_skew, bandage_image, PlasFlow, tab2fasta, fasta2tab, gff2bed1, nanoplot, Grep1, tp_cat, flye, bg_column_arrange_by_header, Filter1, tp_cut_tool, staramr_search, ncbi_blastn_wrapper, regex1, deeptools_bam_coverage |
Genome annotation, Genome visualisation, Mapping assembly, Gene prediction, Cross-assembly, Box-Whisker plot plotting, Sequence visualisation, Sequence analysis, Antimicrobial resistance prediction, Scatter plot plotting, Genome assembly, Pairwise sequence alignment, Coding region prediction, Base-calling, Variant calling, Sequence assembly, Sequence assembly visualisation, De-novo assembly |
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|
|
|
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 |
|
snp_sites, tp_cat, bcftools_consensus, 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__, tb_variant_filter, snippy, trimmomatic |
Phylogenetic tree generation, Variant calling, 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 |
|
tp_replace_in_line, tp_grep_tool, tb_profiler_profile, __MERGE_COLLECTION__, addName, tp_sed_tool, tp_cat, 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 |
|
snpSift_filter, bcftools_view, tp_awk_tool, freebayes, vcf2tsv, bowtie2, bcftools_norm |
Statistical calculation, Read mapping, Variant calling |
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|
|
|
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 |
|
collection_element_identifiers, collapse_dataset, samtools_coverage, tp_cat, freebayes, vcf2tsv, bowtie2, bcftools_norm, samtools_depth |
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 |
|
collection_element_identifiers, multiqc, __MERGE_COLLECTION__, __FLATTEN__, checkm2, regex1, __RELABEL_FROM_FILE__ |
Sequencing quality control, Sequence assembly validation, Sequence composition calculation, Validation, Statistical calculation |
|
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 |
|
collection_element_identifiers, multiqc, __MERGE_COLLECTION__, __FLATTEN__, checkm2, regex1, __RELABEL_FROM_FILE__ |
Sequencing quality control, Sequence assembly validation, Sequence composition calculation, Validation, Statistical calculation |
|
MIT |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 (release v0.1) |
https://usegalaxy.org |
8e863bbef37cc36b |
https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, metagenomics, amplicon, name:microgalaxy |
2025-02-06 |
2025-04-25 |
1 |
1 |
|
fastq_dl, __MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz |
|
|
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, bedtools_maskfastabed, mapseq, taxonomy_krona_chart, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, biom_convert |
k-mer counting, Mapping, Formatting, Visualisation |
|
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, __UNZIP_COLLECTION__, fastq_filter, multiqc, fastqc, fastp, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace, mgnify_seqprep |
Sequencing quality control, Validation, Nucleic acid design, Statistical calculation, Sequence contamination filtering, Sequence trimming, Read pre-processing, 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 |
|
prinseq, fastq_filter, multiqc, fastqc, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace |
Sequence contamination filtering, Sequencing quality control, Sequence composition calculation, Sequence trimming, Validation, Read pre-processing, Statistical calculation |
|
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 |
|
snpSift_filter, table_compute, Cut1, collapse_dataset, minimap2, Remove beginning1, CONVERTER_gz_to_uncompressed, Paste1, regexColumn1, clair3, tp_cut_tool, bcftools_consensus, snpSift_extractFields, Count1, samtools_coverage, bcftools_norm, samtools_depth, tp_head_tool |
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, multiqc, fastqc, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace |
Sequence contamination filtering, Sequencing quality control, Sequence composition calculation, Sequence trimming, Validation, Read pre-processing, Statistical calculation |
|
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 |
|
snpSift_filter, table_compute, Cut1, collapse_dataset, minimap2, Remove beginning1, CONVERTER_gz_to_uncompressed, Paste1, regexColumn1, clair3, tp_cut_tool, bcftools_consensus, snpSift_extractFields, Count1, samtools_coverage, bcftools_norm, samtools_depth, tp_head_tool |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |
|
MGnify's amplicon pipeline v5.0 (release v0.2) |
https://usegalaxy.org |
77de7101effbff3d |
https://usegalaxy.org/published/workflow?id=77de7101effbff3d |
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep |
mgnify_amplicon, metagenomics, amplicon, name:microgalaxy |
2025-03-13 |
2025-04-25 |
1 |
1 |
|
fastq_dl, __MERGE_COLLECTION__, tp_awk_tool, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz |
|
|
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, bedtools_maskfastabed, mapseq, taxonomy_krona_chart, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, tp_awk_tool, biom_convert |
k-mer counting, Mapping, Formatting, Visualisation |
|
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, __UNZIP_COLLECTION__, fastq_filter, multiqc, fastqc, fastp, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace, mgnify_seqprep |
Sequencing quality control, Validation, Nucleic acid design, Statistical calculation, Sequence contamination filtering, Sequence trimming, Read pre-processing, 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 |
|
prinseq, fastq_filter, multiqc, fastqc, trimmomatic, fastq_to_fasta_python, cshl_fasta_formatter, tp_find_and_replace |
Sequence contamination filtering, Sequencing quality control, Sequence composition calculation, Sequence trimming, Validation, Read pre-processing, Statistical calculation |
|
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 |
|
multiqc, fastqc, Cut1, fastp, bamtools_split_mapped, Add_a_column1, nanoplot, minimap2, Grep1, collapse_dataset, kraken2, krakentools_extract_kraken_reads, regexColumn1, __FILTER_FAILED_DATASETS__, collection_column_join, porechop, samtools_fastx |
Sequencing quality control, Data handling, Box-Whisker plot plotting, Validation, Aggregation, Statistical calculation, Sequence contamination filtering, Scatter plot plotting, Pairwise sequence alignment, Taxonomic classification, Visualisation, Sequence alignment analysis, Sequence composition calculation |
|
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 |
|
collection_element_identifiers, multiqc, __MERGE_COLLECTION__, __FLATTEN__, checkm2, regex1, __RELABEL_FROM_FILE__ |
Sequencing quality control, Sequence assembly validation, Sequence composition calculation, Validation, Statistical calculation |
|
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 |
|
snpSift_filter, table_compute, Cut1, collapse_dataset, minimap2, Remove beginning1, CONVERTER_gz_to_uncompressed, Paste1, regexColumn1, clair3, tp_cut_tool, bcftools_consensus, snpSift_extractFields, Count1, samtools_coverage, bcftools_norm, samtools_depth, tp_head_tool |
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 |
|
snpSift_filter, table_compute, Cut1, collapse_dataset, minimap2, Remove beginning1, CONVERTER_gz_to_uncompressed, Paste1, regexColumn1, clair3, tp_cut_tool, bcftools_consensus, snpSift_extractFields, Count1, samtools_coverage, bcftools_norm, samtools_depth, tp_head_tool |
Pairwise sequence alignment, Variant calling |
|
MIT |
|
|
True |
False |