# Bio Cfdna Preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment...

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## 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 | -80C after extraction | Prevents degradation |

## UMI-Aware Pipeline with fgbio

```bash
# fgbio 3.0+ (actively maintained)

# Step 1: Extract UMIs from reads and annotate
fgbio ExtractUmisFromBam \
    --input raw.bam \
    --output with_umis.bam \
    --read-structure 3M2S+T 3M2S+T \
    --molecular-index-tags ZA ZB \
    --single-tag RX

# 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 \
    --input aligned.bam \
    --output grouped.bam \
    --strategy adjacency \
    --edits 1 \
    --min-map-q 20

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-cfdna-preprocessing/SKILL.md