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bio-cfdna-preprocessing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: fgbio FastqToBam → fgbio GroupReadsByUmi → fgbio CallMolecularConsensusReads.
- Preprocess my cfDNA sequencing data" → Process cell-free DNA reads with UMI extraction, consensus calling, and error suppression for sensitive variant detection. CLI: fgbio FastqToBam → fgbio GroupReadsByUmi → fgbio CallMolecularConsensusReads.
- Preprocess cell-free DNA sequencing data with 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.
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use when processing plasma cfDNA sequencing data before downstream analysis.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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