checkv

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