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数据与复现
BI
bio-genome-assembly-assembly-qc
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Assess assembly quality with QUAST, BUSCO, and NGA50 metrics.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-assembly-qc
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 评估 genome assembly quality ，支持 contiguity metrics (QUAST) 、 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。
原始文档
SKILL.md 摘录
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 |
适用场景
- Use bio-genome-assembly-assembly-qc ，用于 genomics 、 bioinformatics workflows。
- Apply bio-genome-assembly-assembly-qc to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- short-read-assembly - SPAdes assembly
- long-read-assembly - Flye/Canu assembly
- assembly-polishing - Improve accuracy
- metagenomics - Metagenome analysis
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