BWA Aligner Skill
SkillDev toolsBWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection
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Details
Instructions available. Your AI can read the instructions. Execution depends on the setup they require.
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What this skill tells your AI
The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/bwa-aligner/SKILL.md and read by Ahel’s review.
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)
Signals
- GitHub stars
- 2k
- Forks
- 113
- Last commit
- Sep 2026
Advanced
- Item type
- skill
- Key
bwa-aligner- Source
- github.com/a5c-ai/babysitter