An MCP server that enables AI assistants to run FastQC and MultiQC quality control analysis on sequencing data. Part of the [Bio-MCP
An MCP server that enables AI assistants to run FastQC and MultiQC quality control analysis on sequencing data. Part of the [Bio-MCP
The server publishes 11 tools. What each one is for:
fastqc_single_async — Queue single file analysisfastqc_batch_async — Queue batch analysismultiqc_report_async — Queue report generationget_job_status — Check job progressget_job_result — Retrieve completed resultscancel_job — Cancel running jobsPrerequisites — The Prerequisites tool exposed by this serverInstallation — The Installation tool exposed by this serverfastqc_single — The fastqc_single tool exposed by this serverfastqc_batch — The fastqc_batch tool exposed by this servermultiqc_report — The multiqc_report tool exposed by this serverInstallation goes through your MCP client rather than a global install: point it at multiqc on PyPI and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
Configuration is passed through the environment: BIO_MCP_QUEUE_URL, BIO_MCP_FASTQC_PATH, BIO_MCP_MULTIQC_PATH. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.
Install FastQC and MultiQC: ```bash
fastqc_single_async — Queue single file analysisfastqc_batch_async — Queue batch analysismultiqc_report_async — Queue report generationget_job_status — Check job progressget_job_result — Retrieve completed resultscancel_job — Cancel running jobsfastqc_single — The fastqc_single tool exposed by this server.fastqc_batch — The fastqc_batch tool exposed by this server.multiqc_report — The multiqc_report tool exposed by this server.Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.
Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.
| Tool | What it does |
|---|---|
| fastqc_single_async | Queue single file analysis |
| fastqc_batch_async | Queue batch analysis |
| multiqc_report_async | Queue report generation |
| get_job_status | Check job progress |
| get_job_result | Retrieve completed results |
| cancel_job | Cancel running jobs |
| fastqc_single | The fastqc_single tool exposed by this server. |
| fastqc_batch | The fastqc_batch tool exposed by this server. |
| multiqc_report | The multiqc_report tool exposed by this server. |
{
"mcpServers": {
"bio-fastqc": {
"command": "python",
"args": [
"-m",
"src.server"
],
"cwd": "/path/to/bio-mcp-fastqc"
}
}
}From the project documentation. Replace placeholders and example paths before connecting.
Install FastQC and MultiQC: ```bash
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