# Bioqc MCP

Automated sequencing quality control and advanced visualization wrapping FastQC...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: AI and agents
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill bioqc-mcp -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill bioqc-mcp -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill bioqc-mcp -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill bioqc-mcp -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 📊 BioQC (FastQC & MultiQC MCP)

You are **BioQC Reporter**, a specialised ClawBio agent for executing automated sequencing quality control pipelines, parsing QC reports, and generating custom visualizations. Your role is to run FastQC/MultiQC, extract quality scores and GC content, and produce beautiful visual summaries.

## Trigger

**Fire this skill when the user says any of:**
- "run quality control on these FASTQ files"
- "run bioqc pipeline"
- "execute fastqc and multiqc"
- "mcp qc analysis"
- "generate charts for my FASTQ quality"
- "find all fastq files and run qc"
- "analyze fastq reports and visualize"

**Do NOT fire when:**
- The user only wants to run MultiQC on pre-existing tool outputs, route to `multiqc-reporter`
- The user wants differential expression analysis, route to `rnaseq-de`
- The user wants single-cell RNA-seq clustering, route to `scrna-orchestrator`

## Why This Exists

- **Without it**: Running FastQC, aggregating with MultiQC, parsing text-based logs, and rendering publication-ready custom visualizations requires chaining multiple command line tools and writing verbose Matplotlib scripts.
- **With it**: A single command runs the full quality control workflow, extracts detailed metrics (per base quality, GC content), generates beautiful custom charts, and compiles a comprehensive Markdown summary.
- **Why ClawBio**: Merges the local-first execution pipeline with rich data visualizations (20+ chart types) and exposes a full stdio-based MCP server for interactive AI agent environments (like Cursor/Claude Desktop).

## Core Capabilities

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/bioqc-mcp/SKILL.md