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GPU-Euler: Sequence Assembly Using GPGPU

Syed F. Mahmood, Huzefa Rangwala
George Mason University
IEEE 13th International Conference on High Performance Computing and Communications (HPCC), 2011

@inproceedings{mahmood2011gpu,

   title={GPU-Euler: Sequence Assembly Using GPGPU},

   author={Mahmood, S.F. and Rangwala, H.},

   booktitle={High Performance Computing and Communications (HPCC), 2011 IEEE 13th International Conference on},

   pages={153–160},

   year={2011},

   organization={IEEE}

}

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Advances in sequencing technologies have revolutionized the field of genomics by providing cost effective and high throughput solutions. In this paper, we develop a parallel sequence assembler implemented on general purpose graphic processor units (GPUs). Our work was largely motivated by a growing need in the genomic community for sequence assemblers and increasing use of GPUs for general purpose computing applications. We investigated the implementation challenges, and possible solutions for a data parallel approach for sequence assembly. We implemented an Eulerian-based sequence assembler (GPU-Euler) on the nVidia GPUs using the CUDA programming interface. GPU-Euler was benchmarked on three bacterial genomes using input reads representing the new generation of sequencing approaches. Our empirical evaluation showed that GPU-Euler produced lower run times, and comparable performance in terms of contig length statistics to other serial assemblers. We were able to demonstrate the promise of using GPUs for genome assembly, a computationally intensive task.
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