genomad

name	genomad
description	Identify plasmids, viruses, and other mobile genetic elements in assemblies or genomes. Use for plasmidome/virome mining, MGE-aware AMR context, and pre-CheckV viral candidate lists. Upstream: https://github.com/apcamargo/genomad.
license	MIT
category	analysis-tools
tags	["MGE","plasmid","virus","genome-mining"]
upstream	https://github.com/apcamargo/genomad
stage	mining

geNomad

Upstream: apcamargo/genomad

Citation

Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303–1312 (2024). https://doi.org/10.1038/s41587-023-01953-y

Analytical thinking

geNomad scores contigs/genomes for plasmid-like and virus-like signals using markers + neural networks. Use it to:

1. Flag MGEs before interpreting chromosomal BGCs/AMR
2. Build viral candidate sets for checkv
3. Separate plasmid-borne ARGs (rgi hits on plasmid contigs)

Do not equate “plasmid score high” with a complete circular plasmid. For viruses, always run CheckV before publishing vMAG completeness. For finer MGE detail use mobileog (proteins), isescan (IS), integronfinder (integrons), and mob-suite (MOB/replicon typing) or plasmidfinder / staramr (CGE replicons).

Can run on full assemblies (pre-binning) or on bins; pre-binning catches MGEs that never enter bacterial bins.

Prerequisites

Requirement	Minimum	Recommended
DB	genomad download-database	Pin path + version
Input	Contigs or genomes FASTA
CPU	8	16+
Disk	DB tens of GB class	SSD helpful

How to run

conda install -c bioconda genomad
genomad download-database db/genomad

genomad end-to-end \
  contigs.fa \
  temp/genomad/${id} \
  -d db/genomad \
  --threads 16 \
  --cleanup

# Key tables (names may include sample prefix)
# temp/genomad/${id}/${id}_summary/${id}_virus_summary.tsv
# temp/genomad/${id}/${id}_summary/${id}_plasmid_summary.tsv

Key parameters

Option	Guidance
--splits	Lower memory on huge assemblies (see docs)
--cleanup	Remove intermediate heavy files
score cutoffs	Filter summary TSVs for reporting

Decision tree

MGE / virus goal?
├─ Plasmid + virus screen on assembly → genomad
├─ Virus-focused legacy SOP → virsorter2 (± genomad consensus)
└─ Publish viral genomes → checkv quality mandatory

Troubleshooting

Symptom	Action
DB path errors	Absolute path to downloaded DB
Memory errors	--splits / smaller input chunks
Empty virus table	Low viral signal or too-short contigs — check min length filters

Related skills

checkv · virsorter2 · vcontact · plasmaag · mobileog · isescan · integronfinder · mob-suite · cge-finders · plasmidfinder · staramr · rgi · resfinder · antismash · microbial-mining · megahit