archaic-introgression
Detect Neanderthal and Denisovan introgression segments from modern human genomes
npx skills add BioTender-max/awesome-bio-agent-skills --skill archaic-introgression --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Archaic Introgression Detector ## Trigger **Fire when:** - User asks about Neanderthal or Denisovan DNA in modern humans - User wants to detect archaic introgression segments - User mentions IBDmix, Sprime, or hmmix methods - User has modern + archaic VCF files and wants to compare them **Do NOT fire when:** - User asks about general ancestry or population structure (use claw-ancestry-pca) - User asks about pharmacogenomics or clinical variants - User wants admixture proportions without segment-level detail ## Why This Exists Between 1-4% of non-African modern human genomes derive from archaic hominins (Neanderthals, Denisovans). Identifying these segments matters for understanding human evolution, disease susceptibility, and immune adaptation. Three complementary methods exist (IBDmix, Sprime, hmmix), each with different strengths. This skill wraps all three behind a unified interface with a pure-Python fallback when external binaries are unavailable. ## Core Capabilities 1. **IBDmix**: Detect segments shared IBD between modern and archaic genomes using LOD score thresholds 2. **Sprime**: Identify introgressed haplotypes without requiring an archaic reference panel 3. **hmmix**:
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Example Queries
- Output Structure
- JSON structure
- Dependencies
- Gotchas
- Safety
Run with IBDmix on VCF inputs python archaic_introgression.py \ Run demo with synthetic data python archaic_introgression.py --demo --output /tmp/introgression_demo Filter to specific samples Adjust LOD threshold
What does the archaic-introgression skill do?
Detect Neanderthal and Denisovan introgression segments from modern human genomes
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill archaic-introgression --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.