busco

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.
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  # if packaged; else follow upstream

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