busco-status-interpretation
Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. Use when running BUSCO QC, comparing assemblies, or reporting completeness. See also: prokka-genome-annotation for annotation workflows feeding BUSCO.
npx skills add BioTender-max/awesome-bio-agent-skills --skill busco-status-interpretation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# BUSCO Status Interpretation Guide ## Overview BUSCO (Benchmarking Universal Single-Copy Orthologs) is the standard tool for assessing genome, transcriptome, and proteome completeness by searching for conserved single-copy orthologs from the OrthoDB database. Correct interpretation of BUSCO output is essential for genome quality assessment, comparative genomics, and publication-ready reporting. The most common analytical error is excluding Duplicated BUSCOs from completeness counts, which artificially penalizes polyploid organisms and assemblies with legitimate gene duplications. This guide covers BUSCO status categories, output file formats, parsing strategies, cross-proteome comparisons, lineage dataset selection, and common pitfalls in BUSCO interpretation. --- ## Key Concepts ### BUSCO Status Categories BUSCO assigns each searched ortholog one of four statuses: | Status | Abbreviation | Meaning | Count as Complete? | |---|---|---|---| | **Complete (single-copy)** | S | Found exactly once in the genome/proteome | YES | | **Duplicated** | D | Found more than once (multiple copies) | YES | | **Fragmented** | F | Partial match, likely incomplete gene model | NO | | **Missing** | M
- Overview
- Key Concepts
- BUSCO Status Categories
- Why Duplicated Equals Complete
- BUSCO Output Formats
- Decision Framework
- Lineage Dataset Selection
- Best Practices
- Common Pitfalls
- Workflow
- Further Reading
- Related Skills
What does the busco-status-interpretation skill do?
Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. Use when running BUSCO QC, comparing assemblies, or reporting completeness. See also: prokka-genome-annotation for annotation workflows feeding BUSCO.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill busco-status-interpretation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.