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International Symposium on Bioinformatics Research and Applications

ISBRA 2018: Bioinformatics Research and Applications pp 227–232Cite as

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

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Part of the book series: Lecture Notes in Computer Science ((LNBI,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.

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References

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Author information

Authors and Affiliations

  1. Nanjing Gezhi Genomics Bioscience, Inc., Chengdu, 610051, China

    Ke Huang, Shubo Yang, Zhaojian Luo, Ke Yang, Menghan Chen & Guopeng Wei

  2. Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China

    Ke Huang & Jian Huang

Authors
  1. Ke Huang
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  2. Shubo Yang
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  3. Zhaojian Luo
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  4. Ke Yang
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  5. Menghan Chen
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  6. Guopeng Wei
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  7. Jian Huang
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Corresponding author

Correspondence to Jian Huang .

Editor information

Editors and Affiliations

  1. Chinese Academy of Sciences, Beijing, China

    Fa Zhang

  2. Georgia State University, Atlanta, GA, USA

    Zhipeng Cai

  3. Georgia State University, Atlanta, GA, USA

    Pavel Skums

  4. Chinese Academy of Sciences, Beijing, China

    Shihua Zhang

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© 2018 Springer International Publishing AG, part of Springer Nature

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Cite this paper

Huang, K. et al. (2018). A Fast Genome Sequence Aligner Based on Minimal Perfect Hash Algorithm Realized with FPGA Based Heterogeneous Computing Platform. In: Zhang, F., Cai, Z., Skums, P., Zhang, S. (eds) Bioinformatics Research and Applications. ISBRA 2018. Lecture Notes in Computer Science(), vol 10847. Springer, Cham. https://doi.org/10.1007/978-3-319-94968-0_21

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  • DOI: https://doi.org/10.1007/978-3-319-94968-0_21

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-94967-3

  • Online ISBN: 978-3-319-94968-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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