bwa-aligner

# 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)