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Bwa aligner

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/bwa-aligner

BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selectionFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill bwa-aligner

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.6 KB, 196 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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