metagenomic-genes-catalogue/main
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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 | #main/AMR genes detection database | Select the database to identify AMR genes with AMRFinderPlus. |
|
| Metagenomics Trimmed reads | #main/Metagenomics Trimmed reads | Input for this workflow is a paired collection from metagenomics trimmed reads |
|
| Virulence genes detection database | #main/Virulence genes detection database | Select the database to identify virulence genes with ABRicate. |
|
| eggNOG database | #main/eggNOG database | Select the database to identify genes function with eggnogmapper |
|
| mmseqs2 taxonomy DB | #main/mmseqs2 taxonomy DB | Select the database to identify taxonomy with mmseqs2 |
|
| starAMR database | #main/starAMR database | Select the database to identify AMR elements with starAMR. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 |
| 7 | Prodigal Gene Predictor | toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0 |
| 8 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1 |
| 9 | Concatenate datasets | Concatenate CDS from each sample toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0 |
| 10 | MMseqs2 Sequence Clustering | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy0 |
| 11 | Text reformatting | Megahit uses contig names that will be redundant between the samples analyzed, so once grouped, there are several contigs with the same name. For coverm, I don't want this redundancy, so I add a number to make each contig name unique. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 |
| 12 | AMRFinderPlus | toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0 |
| 13 | ABRicate | toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 |
| 14 | staramr | toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3 |
| 15 | eggNOG Mapper | toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy4 |
| 16 | SeqKit translate | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_translate/seqkit_translate/2.10.0+galaxy0 |
| 17 | CoverM contig | toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 |
| 18 | argNorm | toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0 |
| 19 | MMseqs2 Taxonomy Assignments | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_taxonomy_assignment/mmseqs2_taxonomy_assignment/17-b804f+galaxy0 |
| 20 | table rename column | Rename dynamic column 2 toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0 |
| 21 | Cut | Retrieves the column corresponding to the contiguous IDs of the detected antibiotic resistance genes. Cut1 |
| 22 | Krakentools: Convert kraken report file | toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 |
| 23 | Tooldistillator sample collection | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 24 | Join eggnog to AMR | Link the eggnog file with the contigs related to antibiotic resistance genes to obtain information on the genetic context of antibiotic resistance. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2 |
| 25 | Join mmseqs2 to AMR | Link the mmseqs2 taxonomy file with the contigs related to antibiotic resistance genes to obtain information on the taxonomy linked with antibiotic resistance. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2 |
| 26 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 27 | Tooldistillator Summarize collection | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
| 28 | Tooldistillator catalogue | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0 |
| 29 | Tooldistillator Summarize catalogue | toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Abricate Virulence Report | #main/Abricate Virulence Report | n/a |
|
| Amrfinderplus Nucleotide | #main/Amrfinderplus Nucleotide | n/a |
|
| Amrfinderplus Report | #main/Amrfinderplus Report | n/a |
|
| Argnorm AMRfinderplus Report | #main/Argnorm AMRfinderplus Report | n/a |
|
| Blast Hits | #main/Blast Hits | n/a |
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| Concatenate Datasets | #main/Concatenate Datasets | n/a |
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| Contig ID Column | #main/Contig ID Column | n/a |
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| Coverm Coverage Tabular | #main/Coverm Coverage Tabular | n/a |
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| Detailed Summary | #main/Detailed Summary | n/a |
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| Eggnog Annotation Filtered | #main/Eggnog Annotation Filtered | n/a |
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| Eggnog Annotations | #main/Eggnog Annotations | n/a |
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| Eggnog Report Orthologs | #main/Eggnog Report Orthologs | n/a |
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| Eggnog Seed Orthologs | #main/Eggnog Seed Orthologs | n/a |
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| MLST | #main/MLST | n/a |
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| MMseqs2 All Sequences | #main/MMseqs2 All Sequences | n/a |
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| MMseqs2 Cluster Sequences | #main/MMseqs2 Cluster Sequences | n/a |
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| MMseqs2 Representative Sequences | #main/MMseqs2 Representative Sequences | n/a |
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| MMseqs2 Taxonomy Filtered | #main/MMseqs2 Taxonomy Filtered | n/a |
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| MMseqs2 Taxonomy Kraken | #main/MMseqs2 Taxonomy Kraken | n/a |
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| MMseqs2 Taxonomy Krona | #main/MMseqs2 Taxonomy Krona | n/a |
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| MMseqs2 Taxonomy Tabular | #main/MMseqs2 Taxonomy Tabular | n/a |
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| Megahit Contigs Output | #main/Megahit Contigs Output | n/a |
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| Megahit Log Output | #main/Megahit Log Output | n/a |
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| Plasmidfinder | #main/Plasmidfinder | n/a |
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| Pointfinder | #main/Pointfinder | n/a |
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| Prodigal Genes Coordinates | #main/Prodigal Genes Coordinates | n/a |
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| Prodigal Genes Sequences | #main/Prodigal Genes Sequences | n/a |
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| Prodigal Genes Translation | #main/Prodigal Genes Translation | n/a |
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| Prodigal Start Tabular | #main/Prodigal Start Tabular | n/a |
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| Report HTML Meta | #main/Report HTML Meta | n/a |
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| Report Tabular Meta | #main/Report Tabular Meta | n/a |
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| Resfinder | #main/Resfinder | n/a |
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| Seqkit Protein Translation | #main/Seqkit Protein Translation | n/a |
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| Summary | #main/Summary | n/a |
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| Tooldistillator Results Catalogue | #main/Tooldistillator Results Catalogue | n/a |
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| Tooldistillator Results Collection | #main/Tooldistillator Results Collection | n/a |
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| Tooldistillator Summarize Catalogue | #main/Tooldistillator Summarize Catalogue | n/a |
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| Tooldistillator Summarize Collection | #main/Tooldistillator Summarize Collection | n/a |
|
Version History
v1.2.1 (latest) Created 25th Feb 2026 at 03:01 by WorkflowHub Bot
Updated to v1.2.1
Frozen
v1.2.1c5bb240
v1.0 (earliest) Created 30th Nov 2025 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
fde7261
Creators and SubmitterActivity
Views: 1238 Downloads: 9282 Runs: 8
Created: 30th Nov 2025 at 03:01
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