metagenomic-genes-catalogue/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Tests Metagenomic analysis, from raw reads to gene catalog. Uses Megahit to assemble contigs and Prodgial to predict CDSs on contigs to provide the gene catalog. Finally, functional, taxonomic, and antimicrobial resistance information is provided.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AMR genes detection database | AMR genes detection database | Select the database to identify AMR genes with AMRFinderPlus. |
|
| Full genes catalogue | Full genes catalogue | Set it to Yes if you want to have the full gene catalogue. Functionnal and taxonomical annotation are made on full clustered CDS |
|
| Metagenomics Trimmed reads | Metagenomics Trimmed reads | Input for this workflow is a paired collection from metagenomics trimmed reads |
|
| Virulence genes detection database | Virulence genes detection database | Select the database to identify virulence genes with ABRicate. |
|
| eggNOG database | eggNOG database | Select the database to identify genes function with eggnogmapper |
|
| mmseqs2 taxonomy DB | mmseqs2 taxonomy DB | Select the database to identify taxonomy with mmseqs2 |
|
| starAMR database | starAMR database | Select the database to identify AMR elements with starAMR. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 |
| 8 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 9 | FASTA-to-Tabular | Convert to tabular format to make it easier to modify the contig ID. toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 10 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1 |
| 11 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 12 | Add input name as column | Adds the sample name to the column corresponding to the initial ID. Allows you to create a unique ID for each sample. toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.3.0 |
| 13 | Tabular-to-FASTA | Return to the fasta format with unique IDs. toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 14 | Prodigal Gene Predictor | toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0 |
| 15 | Concatenate datasets | Concatenate contigs from each sample toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 |
| 16 | MMseqs2 full catalogue Sequence Clustering | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy1 |
| 17 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 18 | AMRFinderPlus | toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0 |
| 19 | ABRicate | toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0 |
| 20 | staramr | toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.12.3+galaxy0 |
| 21 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 22 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 23 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 24 | argNorm | toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0 |
| 25 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 26 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0 |
| 27 | Genes catalogue AMR specific part | Workflow for retrieving the IDs of contigs and CDSs of antibiotic resistance genes and filtering Prodigal output to retrieve a catalogue of antibiotic resistance genes and potential genes present on the same contig as the ARG. |
| 28 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 29 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 30 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 31 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 32 | MMseqs2 ARGs Sequence Clustering | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy1 |
| 33 | eggNOG Mapper | toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.13+galaxy0 |
| 34 | SeqKit translate | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_translate/seqkit_translate/2.13.0+galaxy0 |
| 35 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 36 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0 |
| 37 | MMseqs2 taxonomy | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_taxonomy_assignment/mmseqs2_taxonomy_assignment/17-b804f+galaxy1 |
| 38 | CoverM contig | toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0 |
| 39 | Krakentools: Convert kraken report file | toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2.1+galaxy0 |
| 40 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 41 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 42 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Megahit Contigs Output | Megahit Contigs Output | n/a |
|
| Report HTML Meta | Report HTML Meta | n/a |
|
| Report Tabular Meta | Report Tabular Meta | n/a |
|
| Megahit output with sample name in ID | Megahit output with sample name in ID | n/a |
|
| Prodigal Genes Sequences | Prodigal Genes Sequences | n/a |
|
| Concatenate Datasets | Concatenate Datasets | n/a |
|
| AMRFinderplus Report | AMRFinderplus Report | n/a |
|
| Abricate Virulence Report | Abricate Virulence Report | n/a |
|
| Detailed Summary | Detailed Summary | n/a |
|
| Resfinder | Resfinder | n/a |
|
| Plasmidfinder | Plasmidfinder | n/a |
|
| AMRfinderplus Concatenated Reports | AMRfinderplus Concatenated Reports | n/a |
|
| ABRicate Virulence Concatenated Reports | ABRicate Virulence Concatenated Reports | n/a |
|
| Argnorm AMRfinderplus Concatenated Reports | Argnorm AMRfinderplus Concatenated Reports | n/a |
|
| FASTA with CDS corresponding and related to ARGs (ARGs and linked to) | FASTA with CDS corresponding and related to ARGs (ARGs and linked to) | n/a |
|
| FASTA with contigs related to ARGs | FASTA with contigs related to ARGs | n/a |
|
| Eggnog Annotations | Eggnog Annotations | n/a |
|
| MMseqs2 representative sequences | MMseqs2 representative sequences | n/a |
|
| MMseqs2 Taxonomy Kraken | MMseqs2 Taxonomy Kraken | n/a |
|
| MMseqs2 Taxonomy Tabular | MMseqs2 Taxonomy Tabular | n/a |
|
| CoverM contig | CoverM contig | n/a |
|
| MMseqs2 Taxonomy Krona | MMseqs2 Taxonomy Krona | n/a |
|
| MultiQC Report | MultiQC Report | n/a |
|
Version History
v1.0 (earliest) Created 30th Nov 2025 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0fde7261
Creators and SubmitterActivity
Views: 2492 Downloads: 13609 Runs: 8
Created: 30th Nov 2025 at 03:01
Annotated Properties
Scientific disciplines
Computer Science
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Advanced People list for this Workflow with search and filtering
https://orcid.org/0009-0005-6834-4058
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
Teams: BiRD
Organizations: Centre National de la Recherche Scientifique
https://orcid.org/0009-0005-6834-4058
Advanced Spaces list for this Workflow with search and filtering
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
Advanced Teams list for this Workflow with search and filtering
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
