# BWA MCP Server

> Use this tool when you need to perform DNA/RNA sequence alignment for genomic analysis, as it solves problems in read mapping and genome assembly by providing indexed reference genomes and supporting both short and long read alignment through BWA-MEM and BWA-backtrack algorithms. It takes in sequence data as input and outputs aligned reads, enabling accurate identification of genomic variations. This tool is ideal for use in bioinformatics and genomics research contexts.

Canonical page: https://skillsregistry.net/skills/bio-mcp-bio-mcp-bwa  
JSON: https://api.skillsregistry.net/v1/skills/bio-mcp-bio-mcp-bwa

## Description

Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.

## Trust

- **Trust score (0–1):** 0.60
- **Verification tier:** unverified

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-05-03

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/wjacjkdhsg)
- **Repository:** <https://github.com/bio-mcp/bio-mcp-bwa>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "bio-mcp-bio-mcp-bwa"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/bio-mcp-bio-mcp-bwa` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/bio-mcp-bio-mcp-bwa/pull`

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