FastQC & MultiQC MCP Server

Example Use Cases

• 1

  Perform automated quality control analysis on sequencing FASTQ files.

• 2

  Generate and interpret FastQC and MultiQC HTML reports programmatically.

• 3

  Create advanced, publication-quality visualizations of sequencing quality metrics.

Description

This MCP server provides a comprehensive pipeline for sequencing data quality control, including automated execution of FastQC and MultiQC tools, HTML report parsing, and advanced data visualization with over 20 chart types. It supports batch processing, multi-sample aggregation, and publication-quality output, enabling efficient and detailed QC workflows. The server integrates seamlessly with Claude Desktop and Cursor IDE, offering code execution mode for significant token savings in complex workflows.