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数据与复现
BI
bio-cfdna-preprocessing
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing
- 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
- CLI：fgbio FastqToBam → fgbio GroupReadsByUmi → fgbio CallMolecularConsensusReads。
- Preprocess my cfDNA sequencing data" → Process cell-free DNA reads ，支持 UMI extraction，consensus calling，、 error suppression ，用于 sensitive variant detection. CLI：fgbio FastqToBam → fgbio GroupReadsByUmi → fgbio CallMolecularConsensusReads。
- Preprocess cell-free DNA sequencing data ，支持 UMI-aware deduplication。
- fgbio ExtractUmisFromBam \ --input raw.bam \ --output with_umis.bam \ --read-structure 3M2S+T 3M2S+T \ --molecular-index-tags ZA ZB \ --single-tag RX。
原始文档
SKILL.md 摘录
Pre-Analytical Considerations
| Factor | Requirement | Rationale |
|---|---|---|
| Collection tube | Streck (7 days) or EDTA (6 hrs) | Prevents cell lysis |
| Processing time | ASAP or per tube specs | Minimizes genomic DNA contamination |
| Hemolysis | Avoid | Releases cellular DNA |
| Storage | -80C after extraction | Prevents degradation |
Use -Y for soft-clipping (preserves UMIs)
bwa mem -t 8 -Y reference.fa with_umis.bam |
samtools view -bS - > aligned.bam
Step 3: Group reads by UMI
fgbio GroupReadsByUmi
--input aligned.bam
--output grouped.bam
--strategy adjacency
--edits 1
--min-map-q 20
适用场景
- 适合在processing plasma cfDNA sequencing data before downstream analysis时使用。
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
- fragment-analysis - Analyze fragmentomics after preprocessing
- tumor-fraction-estimation - Estimate ctDNA from sWGS
- ctdna-mutation-detection - Detect mutations from panel data
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