Phage and virus biology · Software
geNomad
Identifies plasmids and viruses in sequencing data, predicts proviruses, and assigns viral taxonomy.
What geNomad is
geNomad is a command-line software pipeline designed to identify mobile genetic elements—specifically plasmids and viruses—within nucleotide sequencing datasets. Developed by Antonio P. Camargo and colleagues, it addresses the challenge of distinguishing plasmid and viral sequences from host chromosomal DNA across isolate genomes, metagenomes, and metatranscriptomes.
The tool provides automated classification scores along with supplementary analyses, including the detection and excision of integrated proviruses from host contigs, functional gene annotation using curated profile databases, and taxonomic assignment of viral sequences based on the International Committee on Taxonomy of Viruses (ICTV) framework.
How it works
geNomad uses a hybrid classification framework that combines marker-based scoring and neural network-based classification modules. Given an input FASTA file, it executes several steps sequentially: gene calling, functional annotation against a database of chromosome-, plasmid-, and virus-specific protein markers, neural network evaluation, provirus identification, and score aggregation.
The marker module assigns proteins to hallmark and class-specific markers, tracking features like universal single-copy genes (USCGs), antimicrobial resistance (AMR) markers, and conjugation machinery. Post-classification filters are applied by default to eliminate potential false positives, requiring a plasmid or virus score of at least 0.7 and demanding at least one hallmark gene on sequences shorter than 2,500 base pairs. Provirus regions are delineated with coordinate boundaries and automatically excised into separate sequence outputs.
Key facts
- Inputs
- Nucleotide FASTA files (.fna, uncompressed or compressed with .gz, .bz2, or .xz)
- Outputs
- FASTA files (.fna, .faa) of identified viruses, plasmids, and proteins; tabular summaries (.tsv); JSON summary
- Classification targets
- Viruses (including integrated proviruses) and plasmids
- Supported data types
- Isolate genomes, metagenomes, and metatranscriptomes
- Taxonomy standard
- ICTV Taxonomy Release MSL39 (assigned up to family level)
What you can use it for
- Identification of extrachromosomal plasmids and phages
- Detecting free viral genomes and plasmid contigs in metagenomic and isolate sequencing assemblies.
- Provirus discovery and host boundary excision
- Locating prophage regions integrated within host chromosomal sequences and extracting their excision coordinates.
- Viral taxonomic profiling
- Assigning viral contigs to ICTV lineages from realm down to family rank.
- Mobile genetic element functional mapping
- Identifying hallmark genes, conjugation-associated genes via CONJscan profiles, and antimicrobial resistance determinants via NCBIfam-AMRFinder profiles on candidate plasmids and viruses.
Run it here
Ask the research agent and it runs geNomad as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
Try asking
“Run geNomad on my metagenome contigs and list the viral and plasmid sequences it finds.”
Strengths and limits
Good at
- Combines marker-based profiles and neural network classification for hybrid scoring.
- Accepts compressed FASTA inputs directly in .gz, .bz2, and .xz formats.
- Automatically excises integrated proviral sequences into designated output files.
- Supports split-database searches to reduce memory consumption on resource-constrained systems.
- Annotates specific functional traits including conjugation genes and antimicrobial resistance markers.
Watch out for
- Cannot assign viral taxonomy past the family level down to genus or species.
- Database protein profile searches require substantial memory unless split using execution parameters.
- Marker database focuses on classification utility and does not provide exhaustive protein function annotation compared to full Pfam or COG scans.
- Does not determine whether a plasmid with identified conjugation genes is fully conjugative or merely mobilisable without additional tools.
Questions
Can I run geNomad online without installing it?
Ask the research agent and it runs geNomad as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
What licence is geNomad under?
BSD-4-Clause (per the bioconda recipe; the repository's own LICENSE is not SPDX-tagged). The terms are published at https://github.com/apcamargo/genomad.
What sequence formats does geNomad take as input?
It accepts standard nucleotide FASTA files containing isolate or environmental sequences. These files can be uncompressed or compressed using gzip (.gz), bzip2 (.bz2), or xz (.xz).
How deep is the viral taxonomic classification?
Viral taxonomy is assigned up to the family rank according to ICTV MSL39. It leaves genus and species ranks blank.
Why are false discovery rate (FDR) columns reported as NA?
FDR values require score calibration to be enabled. Because score calibration is disabled by default, the FDR column contains NA values unless configured otherwise.
How can memory usage be managed on machines with limited RAM?
Users can supply the --splits option (for example, --splits 8) to divide the protein profile searches into smaller chunks, avoiding out-of-memory errors at the cost of processing speed.
How are proviruses reported differently from extrachromosomal viruses?
Proviruses are tagged with 'Provirus' topology and specific 1-indexed genomic coordinates indicating their location in the host scaffold. Their fasta records are automatically excised from the host contig.
How to cite it
Camargo, A. P., Roux, S., Schulz, 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.
Written from geNomad's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.