Skill v1.0.1
currentAutomated scan100/100+3 new
name: checkv description: > Quality assessment of metagenome-assembled viral genomes. Use for installation, parameter choice, execution, output interpretation, or troubleshooting. license: MIT metadata: version: "1.0.1" metagenomics.category: "analysis-tools" metagenomics.tags: "virus, qc, genome-mining" metagenomics.upstream: "https://bitbucket.org/berkeleylab/checkv" metagenomics.stage: "mining" metagenomics.maturity: "reviewed" metagenomics.last-reviewed: "2026-10-18" metagenomics.command-status: "CLI and utility contracts reviewed; not executed here"
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 |
Validation, recovery, and provenance
Require quality_summary.tsv plus contamination/provirus/complete-genome tables and processed FASTAs produced by the pinned release. Reconcile every input sequence to a quality row or explicit failure, inspect quality category, completeness method/range, contamination, host boundaries, terminal repeats, and warnings, and preserve parent-to-trimmed coordinates. Zero hits can be valid; missing summary output is not.
Run vOTU clustering on the exact quality-gated/trimmed sequences and keep IDs stable. Use a fresh output after changing input or database. Record CheckV and dependency versions, database release/checksum, command, FASTA checksums, and acceptance rule. Completeness and contamination are estimates; CheckV does not establish taxonomy, host, or activity.
Related skills
virome-analysis · votu-workflow · virsorter2 · genomad · mag-qc · microbial-mining · tool-selection · vcontact