BWA-MEM2 — DNA Short-Read Aligner
Overview
BWA-MEM2 aligns short DNA reads (Illumina, 50–250 bp) to a reference genome using the BWT-FM index. It is the standard aligner for whole-genome sequencing (WGS), whole-exome sequencing (WES), ChIP-seq, and ATAC-seq DNA alignment. BWA-MEM2 is 2× faster than the original BWA-MEM while producing identical results. It outputs SAM format with proper read group (@RG) headers required by GATK HaplotypeCaller and Picard tools. For paired-end reads, it
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