pku-embl/metagenomics-skills/checkm2

CheckM2

Upstream: chklovski/CheckM2

Citation

Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203–1212 (2023). https://doi.org/10.1038/s41592-023-01940-w

See also docs/references.md.

Analytical thinking

CheckM1-style tools predict quality from lineage-specific single-copy markers. That fails or becomes overconfident when lineages lack robust marker sets (novel phyla/classes, CPR, etc.). CheckM2 uses gradient-boosting ML on broader genomic features to estimate completeness/contamination without explicit lineage marker sets — the paper emphasizes improved accuracy on taxonomically novel MAGs.

Still:

• Values are filters and reporting metrics, not wet-lab truth.
• Do not silently mix CheckM1 and CheckM2 scores across a study.
• Pair with gunc for chimeric / clade-separated contamination CheckM-style

metrics can miss.

• BASALT refinement entry gates (e.g. comp≥35 / cont≤20) often differ from

publication filters (e.g. ≥90 / ≤5) — state both (mag-qc).

How to run

checkm2 database --download
checkm2 predict --input bins/ --output-directory checkm2_out --threads 16

Key parameters

Validation, recovery, and provenance

Require quality_report.tsv, reconcile every input FASTA to exactly one successful or explicitly failed row, and reject duplicate genome IDs. Inspect completeness, contamination, model/translation-table warnings, genome size and coding density; compare discordant or novel genomes with $gunc, taxonomy, and marker evidence. Apply a predeclared quality policy and retain unrounded values.

Do not merge partial results from different database/software releases. After failure, use a clean output directory or document supported resume behavior. Record CheckM2 version, database release/path/checksum, command, input/output checksums, threads, failed genomes, and threshold decisions. Scores are predictions, not measured percentages.

Related skills

mag-qc · gunc · metawrap · basalt · drep · busco