# bio-mcp-bwa
MCP (Model Context Protocol) server for the BWA (Burrows-Wheeler Aligner) sequence alignment tool.
## Overview
This MCP server provides access to BWA functionality, allowing AI assistants to perform alignment of short and long sequencing reads to a reference genome.
## Features
- **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.
## Installation
### Prerequisites
- Python 3.9+
- BWA installed (`bwa`)
### Install BWA
```bash
# macOS
brew install bwa
# Ubuntu/Debian
sudo apt-get install bwa
# From conda
conda install -c bioconda bwa
```
### Install the MCP server
```bash
git clone https://github.com/bio-mcp/bio-mcp-bwa
cd bio-mcp-bwa
pip install -e .
```
## Configuration
Add to your MCP client configuration (e.g., Claude Desktop `~/Library/Application Support/Claude/claude_desktop_config.json`):
```json
{
"mcpServers": {
"bio-bwa": {
"command": "python",
"args": ["-m", "src.server"],
"cwd": "/path/to/bio-mcp-bwa"
}
}
}
```
### Environment Variables
- `BIO_MCP_MAX_FILE_SIZE`: Maximum input file size in bytes (default: 50GB)
- `BIO_MCP_TIMEOUT`: Command timeout in seconds (default: 3600)
- `BIO_MCP_BWA_PATH`: Path to BWA executable (default: finds in PATH)
- `BIO_MCP_TEMP_DIR`: Temporary directory for processing
## Usage
Once configured, the AI assistant can use the following tools:
### `bwa_index` - Create BWA Index
Create a BWA index for a reference genome.
**Parameters:**
- `reference_fasta` (required): Path to the reference FASTA file.
- `algorithm`: Indexing algorithm (`bwtsw` or `is`). Defaults to `bwtsw` for genomes >2GB.
### `bwa_mem` - Align with BWA-MEM
Align reads using the BWA-MEM algorithm.
**Parameters:**
- `reference` (required): Path to the indexed reference genome.
- `reads1` (required): Path to the first reads file (FASTQ).
- `reads2`: Path to the second reads file for paired-end alignment.
- `threads`: Number of threads to use (default: 4).
- `min_seed_length`: Minimum seed length (default: 19).
- `band_width`: Band width for banded alignment (default: 100).
- `read_group`: Read group header line.
### `bwa_aln` - Find SA Coordinates
Find SA coordinates with the BWA-backtrack algorithm.
**Parameters:**
- `reference` (required): Path to the indexed reference genome.
- `reads` (required): Path to the reads file (FASTQ).
- `threads`: Number of threads to use (default: 4).
- `max_mismatches`: Maximum number of mismatches (default: 4).
- `max_gap_opens`: Maximum number of gap opens (default: 1).
### `bwa_samse` - Generate Single-End SAM
Generate alignments in SAM format for single-end reads.
**Parameters:**
- `reference` (required): Path to the indexed reference genome.
- `sai_file` (required): Path to the .sai file from `bwa_aln`.
- `reads` (required): Path to the original reads file.
### `bwa_sampe` - Generate Paired-End SAM
Generate alignments in SAM format for paired-end reads.
**Parameters:**
- `reference` (required): Path to the indexed reference genome.
- `sai_file1` (required): Path to the .sai file for read 1.
- `sai_file2` (required): Path to the .sai file for read 2.
- `reads1` (required): Path to the reads file 1.
- `reads2` (required): Path to the reads file 2.
## Examples
### Index a reference genome
```
Create a BWA index for the file hg38.fasta.
```
### Align paired-end reads
```
Align the paired-end reads from r1.fastq and r2.fastq to the hg38 reference genome using BWA-MEM.
```
## Development
### Running tests
```bash
pytest tests/
```
### Building Docker image
```bash
docker build -t bio-mcp-bwa .
```
## License
MIT License
