Design · MODEL CONTEXT PROTOCOL
sirusb samtools mcp
A Model Control Protocol implementation for samtools, providing a standardized interface for working with SAM/BAM/CRAM files.
WHAT IT CONNECTS
What sirusb samtools mcp gives an AI Agent
- 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...
- **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
- Clone the repository:
- Install dependencies:
- View BAM file:
- Sort BAM file:
- Index BAM file:
- View specific region with flags:
- Sort by read name:
- Calculate depth with multiple input files:
SECURITY
An MCP listing is not a security review
An MCP server may receive model context, credentials, local files, or permission to call external systems. Review its code, requested environment variables, network behavior, package provenance, and maintenance status before connecting it to an agent.