BWA 全名 Burrow-Wheeler Aligner
- The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases.
- BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate.
- BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.
并且在BWA命令中可以分别调用这三个算法，如：aln/samse/sampe for BWA-backtrack，bwasw for BWA-SW，mem for the BWA-MEM