Genomic Agent Discovery
AI agents that collaborate to analyze your DNA. 12 public databases, real-time dashboard, runs 100% locally. Drop in your 23andMe, AncestryDNA, or VCF file.
Install / Use
/learn @HelixGenomics/Genomic Agent DiscoveryQuality Score
Category
Development & EngineeringSupported Platforms
README
Upload your raw DNA file from 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA, or any VCF -- and watch a team of AI agents fan out across 12+ public genomics databases, share discoveries with each other in real time, and produce a comprehensive health report. Everything runs on your machine. Nothing is uploaded anywhere.
<p align="center"> <img src="docs/screenshots/gif-pipeline-running.gif" alt="Pipeline running — agents analyzing, findings arriving, inter-agent chat" width="720"> <br> <em>Real-time pipeline: 7 agents collaborating on a cancer genomics analysis</em> </p>Quick Start
Have a Claude Pro or Max subscription? (Recommended)
No API key needed. Your subscription covers everything.
# 1. Install Claude CLI if you haven't already
npm install -g @anthropic-ai/claude-code
# 2. Log in once — opens browser OAuth (free, uses your Claude Pro/Max subscription)
claude login
# 3. Clone, build, and run
git clone https://github.com/HelixGenomics/Genomic-Agent-Discovery.git
cd Genomic-Agent-Discovery
npm install && npm run build-db
npm start -- --dna ~/Downloads/my-dna-raw.txt
A dashboard opens in your browser and you can watch the agents work. That's it — no API keys, no per-token charges.
Dashboard-first mode: Want to configure everything in the browser first?
npm start -- --serve
# Opens http://localhost:3000 — select your DNA file, pick a preset, customize agents, then click Start
Using an Anthropic API key instead
export ANTHROPIC_API_KEY=sk-ant-... # get one at console.anthropic.com
git clone https://github.com/HelixGenomics/Genomic-Agent-Discovery.git
cd Genomic-Agent-Discovery
npm install && npm run build-db
npm start -- --dna ~/Downloads/my-dna-raw.txt --provider anthropic-api
Typical cost: $1–5 per analysis run depending on preset. See Provider options for OpenAI, Gemini, Ollama, and others.
Dashboard
The dashboard is a real-time mission control for your genomic analysis. It provides full visibility into agent status, findings, inter-agent communication, and costs — all in a single page.
Setup Panel
When you launch the dashboard, you'll see the setup panel where you configure your analysis before starting.
<p align="center"> <img src="docs/screenshots/01-setup-panel.png" alt="Dashboard setup panel" width="720"> <br> <em>Setup panel — select a preset, configure settings, and start your analysis</em> </p>Preset Selection
Choose from 6 built-in research presets, each tuned for a specific domain. Selecting a preset instantly configures the agent pipeline, prompts, models, and focus areas.
<p align="center"> <img src="docs/screenshots/-preset-switching.gif" alt="Switching between presets" width="720"> <br> <em>Switch between presets — each configures a different agent team with specialized prompts</em> </p>Available presets:
| Preset | Agents | Est. Cost | Focus | |--------|--------|-----------|-------| | Quick Scan ⚡ | 2 | $0.05–0.10 | Fast overview across all domains | | Cancer Research 🔬 | 7 | $0.50–2.00 | Deep cancer & tumor genetics with DPYD safety, platinum chemo, immunotherapy, and targeted therapy agents | | Cardiovascular ❤️ | 6 | $0.30–1.00 | Lipid genetics, arrhythmia risk, coagulation, and structural heart | | Pharmacogenomics 💊 | 4 | $0.20–0.80 | CYP enzyme panel, drug transporters, and full CPIC pharmacogene coverage | | Rare Disease 🧬 | 7 | $0.40–1.50 | Metabolic disorders, neurological conditions, connective tissue, immunodeficiency, and rare cancer syndromes | | Custom ⚙️ | You decide | Varies | Build your own agent pipeline from scratch |
Database Status
The setup panel shows a live view of your annotation databases — which are loaded, how many rows each contains, and the total database size. This tells you at a glance whether you need to run npm run build-db.
Editable Agent Prompts & Tier Grouping
Every preset shows its agents grouped by tier: Collection (cheap models, high tool calls), Synthesis (smarter models combining findings), and Report (final output). Click any agent to expand and edit its prompt, change its model, or adjust settings.
<p align="center"> <img src="docs/screenshots/05-editable-agent-prompts.png" alt="Editable agent prompts with tier grouping" width="720"> <br> <em>Cancer preset — 5 haiku collectors, 1 sonnet synthesizer, 1 haiku report writer. All prompts editable.</em> </p> <p align="center"> <img src="docs/screenshots/06-tier-grouping.png" alt="Tier grouping showing collection, synthesis, and report phases" width="720"> <br> <em>Tiered pipeline: cheap models do high-volume database queries, expensive models synthesize findings</em> </p>Template Import & Export
Share your custom agent configurations as JSON template files. Export your current setup (including any prompt edits) and import templates shared by others.
<p align="center"> <img src="docs/screenshots/04-template-import-export.png" alt="Template import and export buttons" width="720"> <br> <em>Import/Export buttons below the preset selector — share templates as JSON files</em> </p>Templates include all agents, prompts, model assignments, and settings. An example Debendox/Trisomy 9 investigation template is included in config/templates/.
Output Configuration
Toggle markdown output and set a shared output directory for all agent reports. Files are named automatically based on agent IDs (e.g., cancer-collector.md, synthesizer.md).
The default output directory is MD_DOCS/ in your repo root. Edit the path to save anywhere. Each agent writes its findings to a separate markdown file.
Pipeline Animation
Once the analysis starts, the dashboard shows a real-time canvas visualization of the agent pipeline. Agents are distributed across concentric rings (scales to 20+ agents), with animated connections showing data flow and collaboration.
<p align="center"> <img src="docs/screenshots/gif-pipeline-running.gif" alt="Full pipeline animation" width="720"> <br> <em>Live pipeline — agents spawn, run, share findings, chat with each other, and complete</em> </p>The pipeline view shows:
- Agent status — spawning (blue pulse), running (green glow), done (solid green), error (red)
- Findings — each discovery appears in real-time with gene, confidence, and clinical category
- Inter-agent chat — agents coordinate in real-time (e.g., cancer agent alerts pharma agent about DPYD variant)
- Cost tracking — estimated cost updates as agents consume tokens
- Log sizes — see how much each agent has written
Full Configuration Walkthrough
<p align="center"> <img src="docs/screenshots/gif-config-walkthrough.gif" alt="Full configuration walkthrough" width="720"> <br> <em>Complete walkthrough of the setup panel — presets, prompts, output, settings, and launch</em> </p>What You Get
A structured genomic health report covering cancer genetics, cardiovascular risk, pharmacogenomics (how you metabolize 100+ drugs), neurological traits, and metabolic health -- all cross-referenced across 12 public databases and prioritized by clinical significance.
A real-time dashboard where you can watch agents query your DNA, discover findings, send messages to each other, and build on each other's research. It looks like a mission control room for your genome.
Raw findings in JSON for downstream analysis, integration with other tools, or building your own visualizations.
What the agents actually do
- Parse your raw DNA file (600K-5M+ variants depending on source)
- Query each variant against ClinVar, GWAS Catalog, AlphaMissense, CADD, PharmGKB, CIViC, and more
- Talk to each other -- the cancer agent might tell the pharma agent "this patient has a DPYD variant, check fluorouracil metabolism"
- Deduplicate automatically so you don't get the same finding five times
- Synthesize cross-domain patterns a single agent would miss
- Write a clear, readable report with appropriate medical disclaimers
Supported DNA Files
| Format | Provider | Typical Variants | File Extension | |--------|----------|-----------------|----------------| | 23andMe | 23andMe | ~6
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