llms.txt

# ClawBio

> ClawBio is the first bioinformatics-native AI agent skill library, built on
> OpenClaw. It provides local-first, privacy-focused, reproducible genomic
> analysis through modular skills that any LLM can invoke via CLI or Python API.

## Docs

- [README](README.md): Project overview, quick start, architecture, skill table
- [CLAUDE.md](CLAUDE.md): Agent routing table, CLI reference, demo data, safety rules
- [AGENTS.md](AGENTS.md): Universal guide for AI coding agents (setup, style, workflow)
- [CONTRIBUTING.md](CONTRIBUTING.md): How to contribute a skill, naming conventions, code standards
- [SECURITY-AUDIT.md](SECURITY-AUDIT.md): Security audit results and remediation log
- [SOUL.md](SOUL.md): ClawBio persona and voice
- [Reference Genome](docs/reference-genome.md): Corpas 30x WGS reference genome (CC0, GRCh37, SNPs + indels + SVs + CNVs)

## Skills (MVP)

- [pharmgx-reporter](skills/pharmgx-reporter/SKILL.md): Pharmacogenomics report from 23andMe/AncestryDNA (12 genes, 51 drugs)
- [drug-photo](skills/drug-photo/SKILL.md): Medication photo to personalised PGx dosage card via Claude vision
- [clinpgx](skills/clinpgx/SKILL.md): Gene-drug lookup against ClinPGx/PharmGKB/FDA databases
- [gwas-lookup](skills/gwas-lookup/SKILL.md): Federated variant query across 9 genomic databases
- [gwas-prs](skills/gwas-prs/SKILL.md): Polygenic risk score calculation from DTC genetic data
- [profile-report](skills/profile-report/SKILL.md): Unified personal genomic profile from all skill results
- [genome-compare](skills/genome-compare/SKILL.md): IBS comparison vs George Church + ancestry estimation
- [equity-scorer](skills/equity-scorer/SKILL.md): HEIM equity metrics (FST, heterozygosity, representation)
- [nutrigx_advisor](skills/nutrigx_advisor/SKILL.md): Nutrigenomics advisor (diet, vitamins, caffeine, lactose)
- [claw-ancestry-pca](skills/claw-ancestry-pca/SKILL.md): PCA against SGDP reference panel (345 samples, 164 populations)
- [claw-semantic-sim](skills/claw-semantic-sim/SKILL.md): Semantic Isolation Index for disease research equity
- [claw-metagenomics](skills/claw-metagenomics/SKILL.md): Metagenomic profiling with Kraken2, RGI/CARD, HUMAnN3
- [bio-orchestrator](skills/bio-orchestrator/SKILL.md): Routes queries to the appropriate skill by file type and keywords
- [ukb-navigator](skills/ukb-navigator/SKILL.md): Semantic search across 22k+ UK Biobank fields
- [galaxy-bridge](skills/galaxy-bridge/SKILL.md): Galaxy tool discovery and execution — 8,000+ bioinformatics tools from usegalaxy.org

## Skills (Implemented / Planned Mix)

- [vcf-annotator](skills/vcf-annotator/SKILL.md): VEP, ClinVar, gnomAD variant annotation
- [lit-synthesizer](skills/lit-synthesizer/SKILL.md): PubMed/bioRxiv literature search and LLM summarisation
- [scrna-embedding](skills/scrna-embedding/SKILL.md): scVI/scANVI latent embedding, batch integration, and stable integrated.h5ad export
- [scrna-orchestrator](skills/scrna-orchestrator/SKILL.md): Scanpy single-cell RNA-seq automation with latent downstream mode and contrastive markers
- [struct-predictor](skills/struct-predictor/SKILL.md): AlphaFold/Boltz protein structure prediction
- [repro-enforcer](skills/repro-enforcer/SKILL.md): Conda/Singularity/Nextflow reproducibility export
- [seq-wrangler](skills/seq-wrangler/SKILL.md): FASTQ/BAM QC and alignment
- [labstep](skills/labstep/SKILL.md): Lab notebook integration

## Optional

- [Skill Catalog (JSON)](skills/catalog.json): Machine-readable index of all skills
- [Skill Template](templates/SKILL-TEMPLATE.md): Template for creating new skills
- [Main CLI](clawbio.py): `python clawbio.py list` / `python clawbio.py run <skill> --demo`