| name | checkv |
| description | Quality assessment of metagenome-assembled viral genomes. Use this skill when working with checkv: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://bitbucket.org/berkeleylab/checkv. For routing across mining tasks use microbial-mining. For stage order use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["virus","qc","genome-mining"] |
| upstream | https://bitbucket.org/berkeleylab/checkv |
| stage | mining |
CheckV
Upstream: CheckV
Citation
Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578–585 (2021). https://doi.org/10.1038/s41587-020-00774-7
See also docs/references.md.
Analytical thinking
Prokaryotic CheckM/CheckM2 marker logic does not transfer to viruses. CheckV
estimates viral genome completeness/contamination using viral-specific AAI
databases and contig QC, guiding which viral MAGs/contigs to trust.
Use after genomad / virsorter2 (or similar) nomination. Always report CheckV
DB version. Completeness tiers in the paper (e.g. high-/medium-quality viral
genomes) should be stated explicitly in Methods — do not call every viral hit a
“complete phage genome.”
Host prediction / taxonomy are separate tools; CheckV is quality-centric.
How to run
checkv end_to_end viral_contigs.fa temp/checkv -t 16 -d $CHECKVDB
Key parameters
| Item | Notes |
|---|
$CHECKVDB | Required — pin release |
| Input | Putative viral sequences from VirSorter2/geNomad |
| Output tiers | Use CheckV quality categories in Results filters |
Related skills
virsorter2 · genomad · mag-qc · microbial-mining · tool-selection
vcontact
