MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool.
If you already use Bio MCP Bwa, the bio mcp bwa mcp server is the piece that lets your assistant work with it directly. MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool.
This MCP server provides access to BWA functionality, allowing AI assistants to perform alignment of short and long sequencing reads to a reference genome.
The toolset is worth reading before you wire it up, because it tells you what the integration is really for:
Prerequisites — The Prerequisites tool exposed by this serverConfiguration is passed through the environment: BIO_MCP_BWA_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.
bwa)Setup follows the usual MCP pattern — install or clone the server, register it in your client's configuration file, restart the client. The configuration blocks on this page cover the common clients.
This sits in the developer tooling group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. Bio MCP Bwa's toolset — Prerequisites — 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.
This entry was verified against Bio MCP Bwa's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| Tool | What it does |
|---|---|
| Prerequisites | The Prerequisites tool exposed by this server. |
{
"mcpServers": {
"bio-bwa": {
"command": "python",
"args": ["-m", "src.server"],
"cwd": "/path/to/bio-mcp-bwa"
}
}
}Configuration as documented by the project. Restart the client after saving.
bwa)| Variable | Description | Required |
|---|---|---|
| BIO_MCP_BWA_PATH | Filesystem location the server is allowed to use. | Optional |
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