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bio-genome-assembly-assembly-qc
Maintainer FreedomIntelligence · Last updated April 1, 2026
Assess assembly quality with QUAST, BUSCO, and NGA50 metrics.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-assembly-qc
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Evaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
- echo "Running QUAST..." if [ -n "$REFERENCE" ]; then quast.py $ASSEMBLY -r $REFERENCE -o ${OUTDIR}/quast -t 8 else quast.py $ASSEMBLY -o ${OUTDIR}/quast -t 8 fi.
Source Doc
Excerpt From SKILL.md
Key Metrics
| Metric | Good Assembly |
|---|---|
| N50 | High (relative to genome) |
| L50 | Low |
| Contigs | Few |
| Misassemblies | 0 (with reference) |
| BUSCO Complete | >95% |
| BUSCO Duplicated | <5% (unless polyploid) |
Key Options
| Option | Description |
|---|---|
-o | Output directory |
-r | Reference genome |
-g | Gene annotations (GFF) |
-t | Threads |
-m | Min contig length (default: 500) |
--large | For large genomes (>100Mb) |
--fragmented | For highly fragmented assemblies |
--scaffolds | Input is scaffolds (includes N-gaps) |
Key Output Metrics
| Metric | Description |
|---|---|
| Total length | Sum of contig lengths |
| # contigs | Number of contigs (>= min length) |
| Largest contig | Length of largest contig |
| N50 | 50% of assembly in contigs >= this length |
| N90 | 90% of assembly in contigs >= this length |
| L50 | Number of contigs comprising N50 |
| GC % | GC content |
| # misassemblies | With reference: structural errors |
| Genome fraction | With reference: % of reference covered |
Use cases
- Use bio-genome-assembly-assembly-qc for genomics and bioinformatics workflows.
- Apply bio-genome-assembly-assembly-qc to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- short-read-assembly - SPAdes assembly
- long-read-assembly - Flye/Canu assembly
- assembly-polishing - Improve accuracy
- metagenomics - Metagenome analysis
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