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align=\"center\"\u003e\n  \u003cimg src=\"assets/blugen-logo.png\" alt=\"BlueGen Logo\" width=\"300\"\u003e\n\u003c/p\u003e\n\n# 🧬 BlueGen\n\n**Personal Genomics Platform** — Powered by the PRSKit polygenic risk score engine.\n\n[![Python](https://img.shields.io/badge/python-3.10+-blue)](https://www.python.org/)\n[![License](https://img.shields.io/badge/license-MIT-green)](LICENSE)\n[![Version](https://img.shields.io/badge/version-1.1.0-orange)]()\n[![PRSKit](https://img.shields.io/badge/engine-PRSKit-purple)]()\n\nTurn a WGS VCF into a comprehensive personal genomics report: polygenic risk scores, pathogenic variants, pharmacogenomics, ancestry, and wellness traits — all offline, all free.\n\n## 🚀 Quick Start\n\n```bash\ngit clone https://github.com/danielperez9430/BlueGen.git\ncd BlueGen\npython3 -m venv venv \u0026\u0026 source venv/bin/activate\npip install -r prs_research_pipeline/requirements.txt\n\n# Full analysis\npython3 prs.py run --full --vcf your_sample.vcf.gz\n\n# Interactive dashboard\nvenv/bin/streamlit run dashboard.py\n```\n\n## 📊 What It Does\n\n| Module | Description | Data Source |\n|--------|-------------|-------------|\n| 🧬 **PRS Engine** | 56 traits, 179 SNPs, population-calibrated z-scores | Curated GWAS + 1000 Genomes |\n| 🔬 **ClinVar** | Pathogenic/likely pathogenic variants with confidence tiers | NCBI ClinVar (4.4M records) |\n| 💊 **PharmGKB** | Drug-gene interactions, CPIC guideline recommendations | CPIC/DPWG (218 guidelines) |\n| 🌍 **Ancestry** | PCA + mtDNA/Y-DNA haplogroups + sub-continental | 1000 Genomes (26 populations) |\n| 🦴 **Archaic DNA** | Neanderthal/Denisovan admixture via AADR direct comparison | Allen Ancient DNA Resource (1.23M SNPs) |\n| 🩺 **PGS Catalog** | 54 published polygenic scores for complex diseases | PGS Catalog (EBI) |\n| 📖 **MedGen** | Disease definitions for ClinVar findings | NCBI MedGen (23K concepts) |\n| 📊 **Dashboard** | 6-page interactive Streamlit app | All JSON outputs |\n\n## 📁 Documentation\n\nFull docs: [`prs_research_pipeline/README.md`](prs_research_pipeline/README.md)\n\nQuick reference: [`USAGE.md`](USAGE.md)\n\nChangelog: [`CHANGELOG.md`](CHANGELOG.md)\n\nData sources: [`prs_research_pipeline/reference/SOURCES.md`](prs_research_pipeline/reference/SOURCES.md)\n\n## 🔧 Requirements\n\n- **Python 3.10+** — `pip install -r prs_research_pipeline/requirements.txt`\n- **PLINK v1.90b7.2+** — [Download](https://www.cog-genomics.org/plink/) (free, GPLv3)\n- **PLINK 2.0** — [Download](https://www.cog-genomics.org/plink/2.0/) (optional, for advanced QC)\n- **bcftools + tabix** — `brew install bcftools tabix` (macOS) or `apt install bcftools tabix` (Linux)\n- **BWA** — `brew install bwa` (optional, for FASTQ → BAM alignment)\n- macOS/Linux (Windows via WSL2)\n- ~200 MB reference data (auto-downloaded on first run)\n- ~65 GB reference data bundle (optional — from [archive.org](https://archive.org/details/bluegen-reference-data) snapshot or `prs_research_pipeline/scripts/setup/` to fetch latest from public sources)\n  - [`bluegen-reference-data`](https://archive.org/details/bluegen-reference-data) — 1000 Genomes, hg19, ClinVar, MedGen, ClinPGx\n  - [`bluegen-pgs-cache`](https://archive.org/details/bluegen-pgs-cache) — 56 PGS Catalog scoring files\n  - [`bluegen-archaic-reference`](https://archive.org/details/bluegen-archaic-reference) — AADR 1240K archaic panel (Neanderthal + Denisovan), pre-converted to PLINK\n  - [`bluegen-vindija-reference`](https://archive.org/details/bluegen-vindija-reference) — Vindija Neanderthal genome VCFs (chr1–22, hg19, ~44 GB)\n  - \u003e **Maintainer:** `python archive_upload.py -j 8` to refresh snapshots\n\n### System Tools\n\nPLINK is **not bundled** — download the correct build for your OS:\n\n| Tool | Version | macOS (Apple Silicon) | macOS (Intel) | Linux |\n|------|---------|----------------------|---------------|-------|\n| PLINK 1.9 | [v1.90b7.2](https://www.cog-genomics.org/plink/) | `plink` (Rosetta) | `plink_mac` | `plink_linux` |\n| PLINK 2.0 | [v2.0.0-a.7.1](https://www.cog-genomics.org/plink/2.0/) | `plink2_mac_arm64` | `plink2_mac` | `plink2_linux` |\n\nPlace the binaries in your `PATH` or symlink them into the project root.\n\n## ⚠️ Disclaimer\n\n**RESEARCH USE ONLY — NOT FOR CLINICAL DIAGNOSIS.** This platform is for research and educational purposes. Clinical decisions should not be based on its output without confirmation by a certified laboratory.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdanielperez9430%2Fbluegen","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdanielperez9430%2Fbluegen","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdanielperez9430%2Fbluegen/lists"}