bio-liquid-biopsy-pipeline
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.
npx skills add BioTender-max/awesome-bio-agent-skills --skill liquid-biopsy-pipeline --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+, VarDict 1.8+, fgbio 2.1+, ichorCNA 0.5+, numpy 1.26+, pandas 2.2+, pysam 0.22+, samtools 1.19+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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. # Liquid Biopsy Analysis Pipeline **"Analyze my liquid biopsy cfDNA data end-to-end"** → Orchestrate UMI-aware preprocessing (fgbio), ctDNA mutation detection (VarDict), tumor fraction estimation (ichorCNA), fragmentomics analysis, and longitudinal monitoring for treatment response. Complete workflow for cfDNA analysis from sequencing to clinical interpretation. ## Pipeline Overview ``` Pre-analytical QC → cfDNA Preprocessing → Fragment QC ↓ ┌─────────────────┴─────────────────┐ ↓ ↓ sWGS Branch Panel Branch ↓ ↓ ichorCNA VarDict/smCounter2 (Tumor Fraction) (
- Version Compatibility
- Pipeline Overview
- Step 0: Pre-Analytical QC
- Step 1: cfDNA Preprocessing with UMI Consensus
- Step 2: Fragment QC Checkpoint
- Step 3a: Tumor Fraction Estimation (sWGS)
- Step 3b: Mutation Detection (Targeted Panel)
- Step 4: CHIP Filtering
- Step 5: Fragmentomics Analysis (Optional)
- Step 6: Longitudinal Tracking
- Complete Pipeline Script
- Related Skills
For UMI-tagged libraries (targeted panels) fgbio pipeline Extract UMIs fgbio ExtractUmisFromBam \ Align bwa mem -t 8 -Y reference.fa with_umis.bam | \ samtools view -bS - > aligned.bam Group by UMI fgbio GroupReadsByUmi \ Consensus calling
What does the bio-liquid-biopsy-pipeline skill do?
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill liquid-biopsy-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.