bioqc-mcp

📊 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

1. Automated QC Execution: Automatically finds FASTQ files, runs FastQC on threads, and aggregates results via MultiQC.
2. Quality Metric Extraction: Parses FastQC summary.txt and fastqc_data.txt to extract exact base quality and GC content distributions.
3. Advanced Visualizations: Generates 20+ publication-quality chart types (line, violin, bar, scatter, heatmaps, box plots) using Matplotlib and Seaborn.
4. Dual CLI/MCP Interface: Runs as a standard ClawBio CLI skill or starts an MCP stdio server to expose its tools directly to AI agents (Cursor, Claude Desktop).