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samtools_mcp

by sirusb
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Python
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SAMtools MCP (Model Control Protocol)

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

Features

  • View and convert SAM/BAM/CRAM files

  • Sort alignment files

  • Index BAM/CRAM files

  • Generate statistics

  • Merge multiple BAM files

  • Calculate read depth

  • Index FASTA files

  • And more...

Core Capabilities

  • File Format Support: Handle SAM (text), BAM (binary), and CRAM (compressed) alignment files

  • Format Conversion: Convert between SAM, BAM, and CRAM formats seamlessly

  • Region-Specific Analysis: Extract and analyze specific genomic regions

  • Flag-Based Filtering: Filter reads based on SAM flags

  • Performance Optimization: Multi-threaded operations for sorting and merging

  • Statistical Analysis: Generate comprehensive alignment statistics

Tools Overview

Tool

Description

Key Features

view

View and convert alignment files

- Format conversion (SAM/BAM/CRAM)

- Region filtering

- Flag-based filtering

- Header manipulation

sort

Sort alignment files

- Coordinate-based sorting

- Name-based sorting

- Memory per thread control

- Multi-threading support

index

Index BAM/CRAM files

- BAI index generation

- CSI index support

- CRAM index creation

merge

Merge multiple BAM/CRAM files

- Multi-file merging

- Thread-enabled processing

- Header reconciliation

depth

Calculate read depth

- Per-base depth calculation

- Region-specific analysis

- Multi-file support

flagstat

Generate alignment statistics

- Comprehensive flag statistics

- Quality checks

- Paired-end metrics

idxstats

BAM/CRAM index statistics

- Reference sequence stats

- Mapped/unmapped counts

- Length information

faidx

Index FASTA files

- FASTA indexing

- Region extraction

- Sequence retrieval

Installation

Using Docker (Recommended)

The easiest way to use SAMtools MCP is through Docker:

# Pull the Docker image docker pull nadhir/samtools-mcp:latest # Run the container docker run -it --rm nadhir/samtools-mcp:latest # To process BAM files, mount a volume: docker run -it --rm -v /path/to/your/bam/files:/data nadhir/samtools-mcp:latest

Local Installation

  1. Clone the repository:

git clone https://github.com/your-username/samtools_mcp.git cd samtools_mcp

  1. Install dependencies:

pip install uv uv pip install -r requirements.txt

Configuration

MCP Server Configuration

To configure the MCP server to use the Docker image, add the following to your MCP configuration file:

{ "servers": { "samtools": { "type": "docker", "image": "nadhir/samtools-mcp:latest", "volumes": [ { "source": "/path/to/your/data", "target": "/data" } ] } } }

Local MCP Configuration

To configure the MCP to run using uv, add the following to your ~/.cursor/mcp.json:

{ "samtools_mcp": { "command": "uv", "args": ["run", "--with", "fastmcp", "fastmcp", "run", "/path/to/samtools_mcp.py"] } }

Replace /path/to/samtools_mcp.py with the actual path to your samtools_mcp.py file.

Usage

Basic Commands

  1. View BAM file:

from samtools_mcp import SamtoolsMCP mcp = SamtoolsMCP() result = mcp.view(input_file="/data/example.bam")

  1. Sort BAM file:

result = mcp.sort(input_file="/data/example.bam", output_file="/data/sorted.bam")

  1. Index BAM file:

result = mcp.index(input_file="/data/sorted.bam")

Advanced Usage

  1. View specific region with flags:

result = mcp.view( input_file="/data/example.bam", region="chr1:1000-2000", flags_required="0x2", output_format="SAM" )

  1. Sort by read name:

result = mcp.sort( input_file="/data/example.bam", output_file="/data/namesorted.bam", sort_by_name=True )

  1. Calculate depth with multiple input files:

result = mcp.depth( input_files=["/data/sample1.bam", "/data/sample2.bam"], region="chr1:1-1000000" )

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

This server cannot be installed

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security - not tested
F
license - not found
-
quality - not tested

How are these scores calculated?

hybrid server

The server is able to function both locally and remotely, depending on the configuration or use case.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

  1. Features
    1. Core Capabilities
    2. Tools Overview
  2. Installation
    1. Using Docker (Recommended)
    2. Local Installation
  3. Configuration
    1. MCP Server Configuration
    2. Local MCP Configuration
  4. Usage
    1. Basic Commands
    2. Advanced Usage
  5. Contributing
    1. License

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