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A Fast Genome Sequence Aligner Based on Minimal Perfect Hash Algorithm Realized with FPGA Based Heterogeneous Computing Platform

  • Ke Huang
  • Shubo Yang
  • Zhaojian Luo
  • Ke Yang
  • Menghan Chen
  • Guopeng Wei
  • Jian HuangEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10847)

Abstract

A fast genome sequence aligner is proposed in this paper. The alignment algorithm is based on minimal perfect hash, reducing the memory occupation and improving memory access efficiency. Several strategies and techniques are adopted to improve the speed and accuracy of the aligner. Realized with a field programmable gate array (FPGA) based heterogeneous computing platform, the aligner achieves similar accuracy compared with BWA-MEM while the speed is around 10 times faster than BWA-MEM.

Keywords

FPGA Minimal perfect hash Fast alignment Smith-Waterman 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Ke Huang
    • 1
    • 2
  • Shubo Yang
    • 1
  • Zhaojian Luo
    • 1
  • Ke Yang
    • 1
  • Menghan Chen
    • 1
  • Guopeng Wei
    • 1
  • Jian Huang
    • 2
    Email author
  1. 1.Nanjing Gezhi Genomics Bioscience, Inc.ChengduChina
  2. 2.Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina

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