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claude-codescience

Babysitter bwa-aligner

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

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/bwa-aligner" ~/.claude/skills/a5c-ai-babysitter-bwa-aligner && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/bwa-aligner/SKILL.md
tags
#sequence-analysis#alignment#genomics#ngs#bioinformatics#alignment-tools
source content

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)