Abstract
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.
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Lu, M., Luo, Q., Wang, B., Wu, J., Zhao, J. (2013). GPU-Accelerated Bidirected De Bruijn Graph Construction for Genome Assembly. In: Ishikawa, Y., Li, J., Wang, W., Zhang, R., Zhang, W. (eds) Web Technologies and Applications. APWeb 2013. Lecture Notes in Computer Science, vol 7808. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37401-2_8
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DOI: https://doi.org/10.1007/978-3-642-37401-2_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-37400-5
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