mBWA: A Massively Parallel Sequence Reads Aligner

  • Yingbo Cui
  • Xiangke Liao
  • Xiaoqian Zhu
  • Bingqiang Wang
  • Shaoliang Peng
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 294)


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.


NGS sequence aligner BWA parallelization MIC coprocessor 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Yingbo Cui
    • 1
  • Xiangke Liao
    • 1
  • Xiaoqian Zhu
    • 1
  • Bingqiang Wang
    • 2
  • Shaoliang Peng
    • 1
  1. 1.National University of Defense TechnologyChangshaChina
  2. 2.BGIShenzhenChina

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