genomix-cli 0.1.0

AI-powered CLI for DNA sequence and genome analysis

Genomix CLI

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AI-powered CLI for DNA sequence and genome analysis.

Genomix is an intelligent command-line tool that helps biologists, bioinformaticians, and researchers analyze genomic data through natural language. Ask questions about your VCF, FASTA, or FASTQ files — the AI reads them, queries real databases (NCBI, Ensembl, ClinVar), and explains results in accessible language.

Local-first. Runs with Ollama by default — your genomic data never leaves your machine.

What It Does

❯ Read raw_variants.vcf and give me a clinical summary

  ⚡ read_file(path='raw_variants.vcf')
    ↳ ##fileformat=VCFv4.2 ...

  1. BRCA1 missense (chr17:43094464): Pathogenic — increased breast/ovarian cancer risk
  2. CFTR deletion (chr7:117559593): Pathogenic — cystic fibrosis (homozygous)
  3. HBB missense (chr11:5226773): Pathogenic — sickle cell trait (carrier)
  4. APOE missense (chr19:44908822): Risk factor — Alzheimer's disease
  ...

❯ What does this reveal about the person's ancestry?

  Based on the variant profile:
  - HBB/rs334 (sickle cell trait): high frequency in African/Mediterranean populations
  - CFTR deltaF508: most common in Northern European populations
  - Combined profile suggests mixed European/African ancestry

Features

• Natural language interface — ask questions about your genomic data in plain English or French
• 9 MCP servers — samtools, BWA, GATK, BLAST+, FastQC, NCBI, Ensembl, ClinVar, dbSNP
• Smart analysis — reads raw VCFs (no annotations needed), identifies genes from coordinates, infers clinical significance
• Ancestry inference — population frequency analysis via gnomAD/1000 Genomes
• 12 built-in skills — specialized AI instructions for sequencing, comparative genomics, and exploration workflows
• 3 AI providers — Ollama/local (default), Claude (Anthropic), OpenAI
• Privacy mode — automatically active with local models, raw sequences never sent to cloud
• Slash commands — /qc, /align, /variant-call, /blast, /msa, /explain, and more
• MCP management — /mcp to view, connect, and manage bioinformatics tool servers

Installation

# Install
pip install genomix-cli

# Check dependencies
genomix setup

# Initialize a project
cd my-analysis/
genomix init

Requirements

• Python 3.11+
• Ollama with a model (e.g., ollama pull qwen3-coder:30b)
• Optional: samtools, BWA, GATK, BLAST+ for bioinformatics tools

Quick Start

# Start interactive mode
genomix

# Non-interactive usage
genomix ask "What is the BRCA1 gene?"
genomix ask "Read sample.vcf and summarize the variants"
genomix run /qc data/reads.fastq.gz

Interactive Session

   ██████╗ ███████╗███╗   ██╗ ██████╗ ███╗   ███╗██╗██╗  ██╗
  ...
  v0.1.0 — AI-powered genome analysis

  ┌──────────────────────────────────────────────────────┐
  │  Project    BRCA Analysis - Cohort 2026              │
  │  Organism   Homo sapiens                             │
  │  Reference  GRCh38                                   │
  │  Provider   opencode (qwen3-coder:30b)               │
  │  Privacy    🔒 ON                                    │
  │  MCP        9 registered (4 connected, 5 missing)    │
  └──────────────────────────────────────────────────────┘

  Connecting MCP servers...
  Connecting to ClinVar... ✓ (3 tools)
  Connecting to dbSNP... ✓ (3 tools)
  Connecting to Ensembl... ✓ (5 tools)
  Connecting to NCBI... ✓ (4 tools)

❯ _

Slash Commands

Command	Description
Analysis
/qc	Quality control (FastQC)
/align	Align reads to reference genome
/variant-call	Call variants (GATK/FreeBayes)
/annotate	Annotate variants (SnpEff/VEP)
/pipeline	Full pipeline: QC → align → call → annotate
Comparative
/blast	BLAST similarity search
/msa	Multiple sequence alignment
/phylo	Phylogenetic tree construction
Exploration
/summary	Summarize a genomic file
/search	Query databases (NCBI, Ensembl...)
/explain	Explain a variant, gene, or region
Session
/mcp	Manage MCP servers (connect, status)
/swarm	Show background analyses
/provider	Switch AI provider
/model	Switch model
/help	Show available commands

Architecture

┌─────────────────────────────────────────────┐
│              genomix-cli                     │
│                                              │
│  CLI/TUI ── Agent Loop ── Swarm Manager      │
│                 │                             │
│    ┌────────────┼────────────┐                │
│    ▼            ▼            ▼                │
│  Tool       Skills       Project              │
│  Registry   System       Manager              │
│    │                                          │
│    ▼                                          │
│  MCP Servers                                  │
│  ├── biotools: samtools, BWA, GATK,           │
│  │   BLAST+, FastQC                           │
│  └── databases: NCBI, Ensembl,                │
│      ClinVar, dbSNP                           │
│                                               │
│  AI Providers                                 │
│  Ollama (local) │ Claude │ OpenAI             │
└───────────────────────────────────────────────┘

Configuration

# ~/.genomix/config.yaml
provider:
  default: opencode        # ollama local (default)
  model: qwen3-coder:30b

# Or use Claude/OpenAI:
# provider:
#   default: claude
#   model: claude-sonnet-4-6

API keys (if using cloud providers):

# ~/.genomix/secrets.yaml (mode 0600)
anthropic_api_key: "sk-ant-..."
openai_api_key: "sk-..."

Contributing

Contributions welcome! This project is in early alpha.

• Spec: docs/superpowers/specs/2026-03-21-genomix-cli-design.md
• Plan: docs/superpowers/plans/2026-03-21-genomix-cli.md
• Skills guide: Create custom skills in .genomix/skills/ following the SKILL.md format

License

Apache 2.0