How do I install the bio mcp bwa mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `BIO_MCP_BWA_PATH` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

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Bio MCP Bwa MCP Server

MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool.

Local serverstdioPython

What is the Bio MCP Bwa MCP Server?

MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool.

What the server does

This MCP server provides access to BWA functionality, allowing AI assistants to perform alignment of short and long sequencing reads to a reference genome.

bwa_index — Create an index for a reference genome
bwa_mem — Align reads using the BWA-MEM algorithm
bwa_aln — Find SA coordinates with the BWA-backtrack algorithm
bwa_samse — Generate single-end alignments in SAM format
bwa_sampe — Generate paired-end alignments in SAM format
Support for large reference genomes and read files

Credentials and setup notes

Python 3.9+ - BWA installed (bwa)

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

How to install the Bio MCP Bwa MCP Server

{
  "mcpServers": {
    "bio-bwa": {
      "command": "python",
      "args": [
        "-m",
        "src.server"
      ],
      "cwd": "/path/to/bio-mcp-bwa"
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Configuration

Python 3.9+ - BWA installed (bwa)

Example prompts to try

“Use Bio MCP Bwa to Prerequisites.”

Frequently asked questions

MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool. Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.