Bioinformatics Agent Skills

By Pipette.bio — Agentic bioinformatics for wet-lab biologists.

Important: The Skill Graph front end server and this repo are maintained by Claude Opus 4.7 (somewhat autonomously).

A hosted MCP server that gives Claude Code (and any MCP client) direct access to a knowledge graph of 78 bioinformatics workflows — single-cell, variant calling, RNA-seq, drug discovery, metagenomics, and more.

Query pipelines mid-conversation. No install. No data download. Just point your AI coding agent at a URL.

🔗 Live graph explorer: skillgraph.pipette.bio 🔗 Main site: pipette.bio

Quick start

1. Add the MCP server to Claude Code

claude mcp add --transport http --scope user skillgraph https://skillgraph.pipette.bio/mcp

Or edit ~/.claude.json manually:

{
  "mcpServers": {
    "skillgraph": {
      "type": "http",
      "url": "https://skillgraph.pipette.bio/mcp"
    }
  }
}

2. Restart Claude Code

MCP servers only load at startup. Fully exit and reopen your session.

3. Verify it’s connected

claude mcp list

You should see:

skillgraph: https://skillgraph.pipette.bio/mcp (HTTP) - ✓ Connected

4. Ask Claude anything

> What tools does the scanpy skill use?
> Find the shortest path from wgs-alignment to pathway-enrichment
> List all single-cell skills
> What comes after variant-calling in a typical pipeline?
> Search for CRISPR-related skills

Claude will call the MCP tools automatically and use the results in its answer.

What’s in the graph

• 78 bioinformatics skills — scanpy, seurat, variant-calling, chipseq, atacseq, gwas-analysis, admet-prediction, molecular-docking, metagenome-binning, and more
• 483 pipeline transitions — each annotated with the data types that flow between steps (BAM, VCF, H5AD, FASTQ, etc.), the number of supporting papers, and whether the edge was confirmed in a curated ground-truth graph
• ~300 tools across skills — Scanpy, Seurat, bwa, samtools, DESeq2, GATK, fastp, MultiQC, STAR, Salmon, Cell Ranger, AlphaFold, AutoDock, and many more
• Full SKILL.md documentation for each skill — triggers, required tools, input/output formats, workflow steps, critical rules, and output artifacts

Tools exposed by the MCP server