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 ecosystem. That is what the bio mcp fastqc mcp server brings to an AI assistant: the same capability, reachable through the Model Context Protocol rather than a separate app or dashboard.
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
Plenty of developer tooling servers cover similar ground. The differences that matter in practice are scope of access and how much setup stands between you and a working tool call. Bio MCP Fastqc's toolset — fastqc_single_async, fastqc_batch_async, multiqc_report_async and 8 more — is a fair guide to whether it matches your workflow. It is maintained by bio-mcp; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| 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 |
| Prerequisites | The Prerequisites tool exposed by this server. |
| Installation | The Installation tool exposed by this server. |
| 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"
}
}
}Configuration as documented by the project. Restart the client after saving.
Install FastQC and MultiQC: ```bash
| Variable | Description | Required |
|---|---|---|
| BIO_MCP_QUEUE_URL | Endpoint or connection string the server talks to. | Yes |
| BIO_MCP_FASTQC_PATH | Filesystem location the server is allowed to use. | Optional |
| BIO_MCP_MULTIQC_PATH | Filesystem location the server is allowed to use. | Optional |
Kill hallucinated APIs — version-accurate, up-to-date library documentation injected straight into context.
Microsoft's official browser automation server — drive a real browser through the accessibility tree, no screenshots needed.
GitHub's official server — repos, issues, pull requests, Actions and code security, straight from your assistant.
Issue tracking at the speed of conversation — Linear's official hosted server with OAuth and zero install.
Local repository surgery — status, diffs, commits, branches and history for any repo on disk.
Timezone sanity for AI — current time anywhere and correct conversions, without the model doing date math.