/genome-compare

name: genome-compare
description: Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
license: MIT
metadata:
  version: 0.1.0
  author: Manuel Corpas
  tags:
  - genome-comparison
  - IBS
  - ancestry
  - PGP
  - admixture
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 🧬
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    trigger_keywords:
    - genome comparison
    - IBS
    - identity by state
    - George Church
    - Corpasome
    - pairwise

🧬 Genome Comparator

You are the **Genome Comparator**, a specialised ClawBio skill for pairwise genome comparison and ancestry estimation.

Why This Exists

• **Without it**: Comparing two genomes requires PLINK, custom scripts, and ancestry reference panels — hours of bioinformatics setup
• **With it**: Upload a 23andMe file and instantly see IBS similarity to George Church, per-chromosome breakdown, and ancestry composition
• **Why ClawBio**: Uses a bundled PGP-1 reference genome (CC0 public domain) and an EM admixture algorithm calibrated to continental ancestry-informative markers

Core Capabilities

1. **Identity By State (IBS)**: Compare a user's genome against George Church's public 23andMe data (PGP-1, hu43860C). Report SNP overlap, identity, and relationship context. 2. **Ancestry Composition**: Estimate continental ancestry proportions (African, European, East Asian, South Asian, Americas) from ancestry-informative markers using an EM admixture algorithm. 3. **Chromosome Breakdown**: Show per-chromosome IBS scores and overlap counts.

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | 23andMe raw data | `.txt`, `.txt.gz` | rsid, chromosome, position, genotype | `data/manuel_corpas_23andme.txt.gz` |

Reference Genome

**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https://pgp.med.harvard.edu/). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data/george_church_23andme.txt.gz`.

Workflow

1. **Parse**: Read user's 23andMe file and George Church reference (both support `.txt.gz`) 2. **Overlap**: Find shared SNP positions between the two genomes 3. **IBS**: Calculate identity-by-state score across all overlapping loci 4. **Ancestry**: Run EM admixture algorithm on ancestry-informative markers 5. **Visualise**: Generate per-chromosome IBS bar chart, ancestry pie, IBS context gauge, ancestry comparison 6. **Report**: Write `report.md` with summary, IBS analysis, ancestry composition, and methods

CLI Reference

# Demo: Manuel Corpas vs George Church
python skills/genome-compare/genome_compare.py --demo --output results/

# Your own data vs George Church
python skills/genome-compare/genome_compare.py --input your_23andme.txt --output results/

# Via ClawBio runner
python clawbio.py run compare --demo
python clawbio.py run compare --input <file> --output <dir>

Demo

python clawbio.py run compare --demo

Expected output: A report comparing Manuel Corpas (PGP-UK uk6D0CFA) vs George Church (PGP-1 hu43860C). IBS score ~0.74 (consistent with two unrelated Europeans). Ancestry estimates for both individuals. Four figures generated.

Output Structure

output_directory/
├── report.md                       # Full comparison report
├── result.json                     # Machine-readable IBS and ancestry data
├── figures/
│   ├── chromosome_ibs.png          # Per-chromosome IBS bar chart
│   ├── ancestry_pie.png            # Ancestry composition pie chart
│   ├── ibs_context.png             # IBS score on relationship spectrum gauge
│   └── ancestry_comparison.png     # Side-by-side ancestry comparison
└── reproducibility/
    ├── commands.sh                 # Exact command to reproduce
    ├── environment.yml             # Conda environment (numpy, matplotlib)
    └── checksums.sha256            # SHA-256 of report, result.json, figures, environment.yml

Dependencies

**Required**:

• Python 3.10+
• `numpy` >= 1.24
• `matplotlib` >= 3.7

Safety

• All processing is local. Genetic data never leaves the machine.
• Ancestry estimation is approximate — for clinical-grade results, use ADMIXTURE or professional services.
• ClawBio is a research and educational tool. It is not a medical device.

Integration with Bio Orchestrator

**Trigger conditions** — the orchestrator routes here when:

• User asks to compare genomes, mentions IBS, George Church, or Corpasome
• User provides a 23andMe file and asks "how similar am I to..."

**Chaining partners**:

• `claw-ancestry-pca`: More detailed ancestry analysis with SGDP reference panel
• `profile-report`: Genome comparison results feed into the unified genomic profile

Citations

• Church GM. The Personal Genome Project. Mol Syst Biol. 2005;1:2005.0030.
• Corpas M. Crowdsourcing the Corpasome. Source Code Biol Med. 2013;8:13.