Date of Award
1-1-2013
Document Type
Open Access Thesis
Department
Computer Science and Engineering
First Advisor
Jason Bakos
Abstract
Advances in next generation sequencing technologies have allowed short reads to be generated at an increasing rate, shifting the bottleneck of the sequencing process to the short read mapping computations. High costs and extended processing times drive researchers to pursue more efficient solutions with an overall goal of a short read mapping architecture capable of processing short reads as they are generated. Digital signal processors have shown high performance capabilities while maintaining low power consumption in a wide field of applications. This thesis explores the use of a DSP accelerated exact match short read mapping algorithm, focusing on a performance metric to increase the number of mapped bases per watt-second. The design is implemented and tested for CPU and alternate coprocessor implementation comparisons to analyze the potential benefit of accelerating a memory bound application.
Rights
© 2013, Shaun I. Gause
Recommended Citation
Gause, S. I.(2013). Accelerating Short Read Mapping Using A DSP Based Coprocessor. (Master's thesis). Retrieved from https://scholarcommons.sc.edu/etd/2351