bwa-aligner

name	bwa-aligner
description	BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["sequence-analysis","alignment","genomics","ngs"]}

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)