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10.1109/HPCC.2011.29guideproceedingsArticle/Chapter ViewAbstractPublication PagesConference Proceedingsacm-pubtype
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GPU-Euler: Sequence Assembly Using GPGPU

Published: 02 September 2011 Publication History

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.

Cited By

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  • (2021)Accelerating large scale de novo metagenome assembly using GPUsProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3458817.3476212(1-11)Online publication date: 14-Nov-2021
  • (2020)PIM-assemblerProceedings of the 57th ACM/EDAC/IEEE Design Automation Conference10.5555/3437539.3437694(1-6)Online publication date: 20-Jul-2020

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Published In

cover image Guide Proceedings
HPCC '11: Proceedings of the 2011 IEEE International Conference on High Performance Computing and Communications
September 2011
1005 pages
ISBN:9780769545387

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IEEE Computer Society

United States

Publication History

Published: 02 September 2011

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  1. Euler tour
  2. GPU
  3. genome assembly

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Cited By

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  • (2021)Accelerating large scale de novo metagenome assembly using GPUsProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3458817.3476212(1-11)Online publication date: 14-Nov-2021
  • (2020)PIM-assemblerProceedings of the 57th ACM/EDAC/IEEE Design Automation Conference10.5555/3437539.3437694(1-6)Online publication date: 20-Jul-2020

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