bwa_indexLABSCO SUMMARY
BWA's real command surface, addressable in conversation.
This does not simplify BWA — the parameters that matter are exposed, and both the MEM and backtrack paths are here, so choosing between them is still your call. What it removes is the shell: an assistant that can already reason about which algorithm suits your read length can now run it against the files you name and hand back the alignment.
What it is
A server around the BWA aligner. It builds the index for a reference genome, aligns reads with the BWA-MEM algorithm, and runs the older backtrack path — finding coordinates first, then producing single-end or paired-end SAM output.
What you get
- An index built for a reference genome, with the indexing algorithm chosen to suit its size
- Reads aligned with BWA-MEM, single or paired end, with seed length, band width, thread count and read group all settable
- The backtrack path: coordinates found with mismatch and gap-open limits under your control
- Single-end and paired-end SAM produced from those coordinates
- Large references and read files handled, with the file-size ceiling and command timeout yours to set
Requirements
BWA installed on the machine and Python for the server. Everything runs locally against files on disk — no account, no key, and no sequence data leaves the machine.
Setup effort
Build from source — clone the repository, then follow the project's own run instructions
USE CASES
01
Getting a reference ready to align against
Build the index once, choosing the algorithm that suits the genome's size.
02
Aligning modern sequencing reads
Run the MEM algorithm against the indexed reference, with seed length and thread count set for the run.
03
Aligning short reads with the older algorithm
Find the coordinates with your mismatch and gap limits, then turn them into single-end alignments.
04
Handling a paired-end run
Produce coordinates for both read files, then combine them into paired-end output.
05
Tagging output with its read group
Set the read group header on the alignment so downstream tools can tell samples apart.
5 tools
Listed in project docs. Your client may show a different list.
bwa_membwa_alnbwa_samsebwa_sampeBEFORE YOU INSTALL
What to know first
Tools you get
5 tools named in the project's documentation.
Requires
- python on PATH
- Python 3.9+
Where it runs
The documented client runs the server on your machine.
INSTALLATION
Connect your client
Server setup
TERMINAL
python -m src.serverMCP Clients
Claude Desktop
CLAUDE DESKTOP · JSON
{
"mcpServers": {
"bio-bwa": {
"command": "python",
"args": [
"-m",
"src.server"
],
"cwd": "<YOUR_PATH_TO_BIO_MCP_BWA>"
}
}
}
