Recipe: Building and Optimizing BWA* ALN 0.5.10 for Intel® Xeon Phi™ Coprocessors

BWA* is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack(ALN), BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the other two for longer sequences ranged from 70bp to 1Mbp.” (

This project, bwa-aln-xeon-phi-0.5.10, optimizes the performance of the BWA 0.5.10 ALN module on both Intel® Xeon® processors and Intel® Xeon Phi™ coprocessors, and supports a symmetric execution model that uses both architectures in cooperation for genome mapping.

The source and ReadMe for this version of BWA ALN 0.5.10 can be downloaded from:

For more complete information about compiler optimizations, see our Optimization Notice.