genome-compare

🧬 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. 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

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.