# Bwa Aligner

> BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection

- Skill: `a5c-ai/bwa-aligner` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/bwa-aligner`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/bwa-aligner/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/bwa-aligner

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# BWA Aligner Skill

## Purpose
Enable BWA-MEM2 alignment for mapping sequencing reads to reference genomes with optimized parameter selection and quality assessment.

## Capabilities
- Read alignment to reference genomes
- Parameter optimization for different read types
- Multi-threading configuration
- Index generation and management
- Alignment quality metrics reporting
- Support for paired-end and single-end reads

## Usage Guidelines
- Generate genome indices before alignment
- Select appropriate parameters for read length and type
- Use multi-threading for performance optimization
- Validate alignment quality metrics post-processing
- Document parameter choices and rationale
- Archive index files for reproducibility

## Dependencies
- BWA-MEM2
- minimap2
- samtools

## Process Integration
- Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
- Long-Read Sequencing Analysis (long-read-analysis)
- Tumor Molecular Profiling (tumor-molecular-profiling)