samtools_mcp
SAMtools MCP for genomic file processing. samtools_mcp is a Model Context Protocol (MCP) server maintained by sirusb. It connects to MCP-compatible clients such as Claude Desktop, Cursor, Cline, and other agents that speak the protocol. It exposes 8 tools, including view, sort, index, merge, depth, flagstat, idxstats and faidx, that an agent can call directly. It is categorized under Tool/Docker and Tool/CLI.
What is this MCP
This MCP provides a standardized interface for working with SAM/BAM/CRAM genomic alignment files, offering format conversion, sorting, indexing, and statistical analysis capabilities.
How to use this MCP
The MCP can be used via Docker (recommended) or local installation. It exposes Python methods for common operations likeview, sort, index, and depth calculations on alignment files.
What this MCP can be used for
This MCP enables genomic researchers to programmatically process alignment files, including format conversion, region-specific analysis, read filtering, and generating comprehensive statistics for SAM/BAM/CRAM files.
AIMCP authority
DR and traffic signal for the AIMCP public domain.
Frequently asked questions
What is the samtools_mcp MCP server?
samtools_mcp is a Model Context Protocol server from sirusb. It lets MCP-compatible AI clients call its tools over a standard interface, so agents like Claude, Cursor, and Cline can use it without custom integration.
How do I connect samtools_mcp to my AI client?
Add samtools_mcp to your client's MCP configuration using the stdio or SSE connection shown in the usage examples on this page, then restart the client to load the server.
What tools does samtools_mcp provide?
samtools_mcp provides 8 tools: view, sort, index, merge, depth, flagstat, idxstats and faidx.
Is samtools_mcp free to use?
samtools_mcp is listed on AIMCP for free. Any API keys or accounts required by the underlying service are set by its provider.
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