The Genomad service uses the genomad tool (https://github.com/apcamargo/genomad) to identify viral, pro-viral, and plasmid contigs in genomic and metagenomic assemblies. The tool employs a hybrid classification approach that combines an alignment-free neural network with a gene-based classifier that utilizes a database of marker protein profiles specific to chromosomes, plasmids, and viruses. Genomad also provides taxonomic assignment of viral genomes using ICTV taxonomy.
The app currently does a simple run of genomad, with no additional processing. In future versions we plan to add viral annotation and our own plasmid classification tools.
The input to the servcie is assembled contigs in fasta format. It will fail with any other file type.
| File Name | Description |
|---|---|
| final.contigs_plasmid.fna | FASTA file containing plasmid contigs |
| final.contigs_plasmid_genes.tsv | Tab-separated file with plasmid gene annotations from prokka |
| final.contigs_plasmid_proteins.faa | FASTA file containing plasmid protein sequences |
| final.contigs_plasmid_summary.tsv | Tab-separated summary file for plasmid contigs |
| final.contigs_summary.json | JSON file containing overall summary of all contigs |
| final.contigs_virus.fna | FASTA file containing viral and pro-viral contigs |
| final.contigs_virus_genes.tsv | Tab-separated file with prokka viral gene annotations |
| final.contigs_virus_proteins.faa | FASTA file containing viral protein sequences |
| final.contigs_virus_summary.tsv | Tab-separated summary file for viral contigs |
| geNomad_run.stderr | Standard error log file from the geNomad run |
The output files are greatly reduced compared to all of the output the genomad command line tool produces. The app pushes these files back into the workspace from the full output directory, so we could add back more of the results files if it is justifiable.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
| Script name | Purpose |
|---|---|
| App-Genomad.pl | App script for the Genomad Service |
Identification of mobile genetic elements with genomad Camargo, A.P., Roux, S., Schultz, F., Babinski, M., Xu, Y., Hu, B., Chain, P. S. G., Nayfach, S., & Kyrpides, N. C., - Nature Biotechnology (2023), DOI: 10.1038./s41587-023-01953-y.