pku-embl/metagenomics-skills/checkv

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

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