ReddRadar
Agent skill
bwa-aligner
BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/bwa-aligner
Metadata
Additional technical details for this skill
- tags
-
sequence-analysis alignment genomics ngs
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
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