DocumentCode :
2091814
Title :
GPU-Euler: Sequence Assembly Using GPGPU
Author :
Mahmood, Syed Faraz ; Rangwala, Huzefa
Author_Institution :
Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
fYear :
2011
fDate :
2-4 Sept. 2011
Firstpage :
153
Lastpage :
160
Abstract :
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.
Keywords :
biology computing; computer graphic equipment; coprocessors; genomics; parallel programming; CUDA programming interface; Eulerian-based sequence assembler; GPGPU; GPU Euler; compute unified device architecture; data parallel approach; general purpose graphic processor unit; genomics; parallel sequence assembler; sequence assembly; Assembly; Data structures; Genomics; Graphics processing unit; Instruction sets; Kernel; Synchronization; Euler tour; GPU; genome assembly;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
High Performance Computing and Communications (HPCC), 2011 IEEE 13th International Conference on
Conference_Location :
Banff, AB
Print_ISBN :
978-1-4577-1564-8
Electronic_ISBN :
978-0-7695-4538-7
Type :
conf
DOI :
10.1109/HPCC.2011.29
Filename :
6062988
Link To Document :
بازگشت