mBWA: A massively parallel sequence reads aligner*

Abstract

Mapping sequenced reads to a reference genome, also known as sequence reads alignment, is central for sequence analysis. Emerging sequencing technologies such as next generation sequencing (NGS) lead to an explosion of sequencing data, which is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a multi-level parallelization strategy to speed up BWA, a widely used sequence alignment tool and developed our massively parallel sequence aligner: mBWA. mBWA contains two levels of parallelization: firstly, parallelization of data input/output (IO) and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by Intel Many Integrated Core (MIC) coprocessor technology. In this paper, we demonstrate that mBWA outperforms BWA by a combination of those techniques. To the best of our knowledge, mBWA is the first sequence alignment tool to run on Intel MIC and it can achieve more than 5-fold speedup over the original BWA while maintaining the alignment precision.