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
# macOS
brew install bwa
# Ubuntu/Debian
sudo apt-get install bwa
# From conda
conda install -c bioconda bwa
Install the MCP server
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):
{
"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 (bwtsworis). Defaults tobwtswfor 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 frombwa_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
pytest tests/
Building Docker image
docker build -t bio-mcp-bwa .
License
MIT License