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数据与复现
BI
bio-genome-assembly-contamination-detection
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Detect and remove contamination in assembled genomes.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-contamination-detection
- 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
- checkm2 predict --input assembly.fa --output-directory checkm2_output --threads 16。
- checkm2 predict --input genomes/ --output-directory checkm2_output \ --threads 16 --extension fa。
原始文档
SKILL.md 摘录
Filter high-quality genomes (MIMAG standards)
awk -F'\t' 'NR==1 || ($2 > 90 && $3 < 5)' quality_report.tsv > high_quality_mags.tsv
Medium quality
awk -F'\t' 'NR==1 || ($2 >= 50 && $3 < 10)' quality_report.tsv > medium_quality_mags.tsv
## Run CheckM lineage workflow
checkm lineage_wf -t 16 -x fa genomes/ checkm_output/
适用场景
- Use bio-genome-assembly-contamination-detection ，用于 genomics 、 bioinformatics workflows。
- Apply bio-genome-assembly-contamination-detection 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
- genome-assembly/assembly-qc - BUSCO and other QC
- genome-assembly/long-read-assembly - Assembly methods
- metagenomics/taxonomic-profiling - Metagenome analysis
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