Efficient parallelization of Bowtie 2 with OpenCL on GPU

As a crucial and computation-intensive aspect in bioinformatics, sequence alignment has gained considerable attention from researchers and developers. Among all the sequence aligners, Bowtie 2 is one of the most commonly used, due to its high speed and accuracy. This thesis presents a parallel implementation of Bowtie 2 with OpenCL, which is a parallel programming model that is becoming widely known and receiving great interest from researchers in recent years. This OpenCL implementation has high portability on various devices, such as multi-core CPU, GPU, and FPGA. This thesis focuses on an efficient and accurate parallelization on GPU. Optimizations that can be accommodated to any devices have been applied, as well as GPU-related optimizations.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Electrical & Computer Engr

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2016

Author dc:creator

• Yan, Yan

Contributors dc:contributor

• Chen, Deming

• OpenCL
• Bowtie 2
• Sequence Aligner
• Smith-Waterman

Statement dc:rights

• Copyright 2016 Yan Yan

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/92977

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/92977