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B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

Yingbo Cui1, Xiangke Liao1, Xiaoqian Zhu2

  • 1School of Computer Science, National University of Defense Technology, Changsha, 410073, China.

Interdisciplinary Sciences, Computational Life Sciences
|September 12, 2015
PubMed
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We developed B-MIC, a novel sequence alignment tool utilizing Intel MIC coprocessors and a three-level parallelization strategy. B-MIC significantly accelerates next-generation sequencing (NGS) data analysis, achieving over fivefold speedup compared to BWA.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Next-generation sequencing (NGS) generates vast amounts of data, overwhelming current sequence alignment tools.
  • Sequence alignment, crucial for mapping sequencing data to reference genomes, has become a computational bottleneck in bioinformatics.
  • Massive computing power is essential to overcome these limitations.

Purpose of the Study:

  • To develop an ultrafast parallel sequence alignment tool (B-MIC) optimized for Intel MIC coprocessors.
  • To address the computational bottleneck in NGS data analysis by accelerating the BWA alignment tool.
  • To leverage the independent nature of sequence reads for efficient parallelization.

Main Methods:

  • Implemented a MIC-oriented, three-level parallelization strategy for the BWA algorithm.
Keywords:
BWAMIC coprocessorMPINGSParallelizationSequence alignerXeon Phi

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  • Developed a three-stage parallel pipeline for data I/O and read alignment.
  • Utilized Intel MIC coprocessor technology and Message Passing Interface (MPI) for inter-node parallelization.

    • Main Results:

    • B-MIC achieves over a fivefold speedup compared to the original BWA.
    • Demonstrated superior performance on Inspur NF5280M servers and the Tianhe-2 supercomputer.
    • Maintained alignment precision while significantly reducing processing time.

    Conclusions:

    • B-MIC is the first sequence alignment tool to effectively utilize Intel MIC architecture.
    • The proposed parallelization strategy significantly enhances the efficiency of NGS data analysis.
    • B-MIC offers a scalable and high-performance solution for sequence alignment challenges.