SCI Skills

EN Index
Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
BI

bio-liquid-biopsy-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Liquid biopsy: cfDNA/ctDNA QC → mutation detection → TMB → MRD.

OpenClawNanoClawAnalysisReproductionbio-liquid-biopsy-pipeline🧠 bioos extended suitebioos extended bioinformatics suiteliquid

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-liquid-biopsy-pipeline

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Complete workflow for cfDNA analysis from sequencing to clinical interpretation.
  • fgbio ExtractUmisFromBam \ --input raw.bam \ --output with_umis.bam \ --read-structure 3M2S+T 3M2S+T \ --single-tag RX.

Source Doc

Excerpt From SKILL.md

Align

bwa mem -t 8 -Y reference.fa with_umis.bam |
samtools view -bS - > aligned.bam

Group by UMI

fgbio GroupReadsByUmi
--input aligned.bam
--output grouped.bam
--strategy adjacency
--edits 1

Consensus calling

fgbio CallMolecularConsensusReads
--input grouped.bam
--output consensus.bam
--min-reads 2

Use cases

  • Use bio-liquid-biopsy-pipeline for genomics and bioinformatics workflows.
  • Apply bio-liquid-biopsy-pipeline to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • liquid-biopsy/cfdna-preprocessing - Preprocessing details
  • liquid-biopsy/tumor-fraction-estimation - ichorCNA analysis
  • liquid-biopsy/ctdna-mutation-detection - Variant calling
  • liquid-biopsy/fragment-analysis - Fragmentomics
  • liquid-biopsy/longitudinal-monitoring - Serial tracking

Related skills

Related skills

Back to directory
AG
Data & ReproBioinformatics & Genomics

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
AL
Data & ReproBioinformatics & Genomics

alpha-vantage

Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.

Claude CodeAnalysis
K-Dense-AI/claude-scientific-skillsView
BI
Data & ReproBioinformatics & Genomics

bio-alignment-filtering

Filter alignments by flag, quality, region, or paired status.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproBioinformatics & Genomics

bio-alignment-indexing

Index BAM/CRAM files with samtools index for random access.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView