GPU-Accelerated Bidirected De Bruijn Graph Construction for Genome Assembly

  • Mian Lu
  • Qiong Luo
  • Bingqiang Wang
  • Junkai Wu
  • Jiuxin Zhao
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7808)


De Bruijn graph construction is a basic component in de novo genome assembly for short reads generated from the second-generation sequencing machines. As this component processes a large amount of data and performs intensive computation, we propose to use the GPU (Graphics Processing Unit) for acceleration. Specifically, we propose a staged algorithm to utilize the GPU for computation over large data sets that do not fit into the GPU memory. We also pipeline the I/O, GPU, and CPU processing to further improve the overall performance. Our preliminary results show that our GPU-accelerated graph construction on an NVIDIA S1070 server achieves a speedup of around two times over previous performance results on a 1024-node IBM Blue Gene/L.


Graphic Processing Unit Genome Assembly Main Memory Graph Construction Chunk Size 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Mian Lu
    • 1
  • Qiong Luo
    • 2
  • Bingqiang Wang
    • 3
  • Junkai Wu
    • 2
  • Jiuxin Zhao
    • 2
  1. 1.A*STAR Institute of High Performance ComputingSingapore
  2. 2.Hong Kong University of Science and TechnologyChina
  3. 3.BGI-ShenzhenChina

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