bio-cfdna-preprocessing
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BWA 0.7.17+, fgbio 2.1+, matplotlib 3.8+, numpy 1.26+, pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # cfDNA Preprocessing **"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. ## 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 | -8
- Version Compatibility
- Pre-Analytical Considerations
- UMI-Aware Pipeline with fgbio
- Python Implementation
- Fragment Size Analysis
- Quality Thresholds
- Related Skills
fgbio 3.0+ (actively maintained) Step 1: Extract UMIs from reads and annotate fgbio ExtractUmisFromBam \ Step 2: Align with BWA-MEM 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 \ Step 4: Call molecular consensus reads
What does the bio-cfdna-preprocessing skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.