| name | checkm2 |
| description | ML-based MAG completeness and contamination estimation. Use this skill when working with checkm2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/chklovski/CheckM2. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["qc","completeness","MAG"] |
| upstream | https://github.com/chklovski/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
| Item | Notes |
|---|
| Database | Pin CheckM2 DB release with software version |
| Input | Directory of bin FASTAs |
| Downstream | Feed filtered bins to drep / gtdbtk |
Related skills
mag-qc · gunc · metawrap · basalt · drep · busco
