| name | busco |
| description | Benchmarking Universal Single-Copy Orthologs for genome completeness. Use this skill when working with busco: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://gitlab.com/ezlab/busco. For stage routing use tool-selection / metagenomics-workflow.
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| license | MIT |
| category | analysis-tools |
| tags | ["qc","completeness","busco"] |
| upstream | https://gitlab.com/ezlab/busco |
| stage | assessment |
BUSCO
Upstream: BUSCO
Citation
Manni, M. et al. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021). https://doi.org/10.1093/molbev/msab199
See also docs/references.md.
Analytical thinking
Useful for isolates/eukaryotes; for prokaryotic MAGs prefer CheckM2 (+ GUNC). Do not mix BUSCO% with CheckM2% unlabeled.
How to run
conda install -c bioconda busco
busco -i genome.fa -l bacteria_odb10 -o temp/busco -m genome -c 16
Key parameters
| -l | lineage DB | Match domain |
| -m | genome/proteins | |
Decision notes
- Stage: assessment (gene-set completeness; complementary to CheckM2 for some lineages)
- Prefer lineage-appropriate BUSCO DB; do not treat BUSCO % as MAG contamination
- Pin software + DB versions in Methods
Related skills
checkm2 · gunc · mag-qc · tool-selection · metagenomics-workflow
