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Agent skill

Genome Compare

by ClawBio in ClawBio/ClawBio

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

MITAuto-check passedResearch & Science

Install Genome Compare

skills CLI
$ npx skills add ClawBio/ClawBio --skill genome-compare -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio genome-compare --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genome-compare .claude/skills/genome-compare && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
genome-compare
GitHub stars
1.2k
Used in
2 other repos
Token cost
~1.2k tokens
SKILL.md length
408 words
Files
9
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

  • Works in 3 steps: Identity By State (IBS): Compare a… → Ancestry Composition: Estimate… → Chromosome Breakdown: Show…
  • Tasks that involve Bioinformatics
  • SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Reference Genome, plus 8 more sections
  • Runs Python scripts from its folder; calls python

What it does

Genome Compare is an agent skill from ClawBio/ClawBio. Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 10 other files (for example `__init__.py`, `api.py` and `data/aims_panel.json`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/genome-compare”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

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

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • pgp.med.harvard.edu

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Genome Compare loads about 1.2k tokens when it runs. Until then it costs about 30 tokens; SKILL.md has 408 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~30
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 408 words, ~1,223 tokens.

Download SKILL.mdSave it as .claude/skills/genome-compare/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.
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
metadata.author
Manuel Corpas
metadata.tags
genome-comparison, IBS, ancestry, PGP, admixture

🧬 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

FormatExtensionRequired FieldsExample
23andMe raw data.txt, .txt.gzrsid, chromosome, position, genotypedata/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
Show full SKILL.md (155 more words)Show less

CLI Reference

bash
# 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

bash
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.

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 8 other files in skills/genome-compare of ClawBio/ClawBio.

  • SKILL.md
  • __init__.py
  • api.py
  • data/aims_panel.json
  • data/george_church_23andme.txt.gz
  • data/manuel_ancestry.json
  • data/manuel_corpas_23andme.txt.gz
  • genome_compare.py
  • tests/test_genome_compare.py

Open the folder on GitHubat commit dece754

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Genome Compare next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Genome Compare compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Genome Compare this skillClawBio/ClawBio1.2k2 repos~1.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Genome Compare

What does Genome Compare do?

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture. Genome Compare is an agent skill from ClawBio/ClawBio.

When should I use Genome Compare?

Genome Compare fits situations like: tasks that involve Bioinformatics.

How do I install Genome Compare in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill genome-compare -a claude-code`. Or copy the skill folder (skills/genome-compare in ClawBio/ClawBio) into .claude/skills/genome-compare in your project. Claude Code loads it when a task matches its description.

How do I install Genome Compare in Codex?

Run `npx skills add ClawBio/ClawBio --skill genome-compare -a codex`. Or copy the skill folder (skills/genome-compare in ClawBio/ClawBio) into .agents/skills/genome-compare in your project. Codex loads it when a task matches its description.

Can I use Genome Compare in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill genome-compare -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/genome-compare, .gemini/skills/genome-compare, .github/skills/genome-compare and .opencode/skills/genome-compare in your project.

What does Genome Compare need to run?

Going by SKILL.md and its folder, Genome Compare needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Genome Compare access the network?

SKILL.md names 1 domain. As links in the text: pgp.med.harvard.edu. This is read from the text; nothing was executed.

Is Genome Compare safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Genome Compare use?

Genome Compare is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Genome Compare use?

About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Genome Compare?

Skills that share tags, products or a category with Genome Compare: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Genome Compare?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.