Efficient parallelization of Bowtie 2 with OpenCL on GPU

Yan, Yan

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https://hdl.handle.net/2142/92977 Copy

Description

Title

Efficient parallelization of Bowtie 2 with OpenCL on GPU

Author(s)

Yan, Yan

Issue Date

2016-07-21

Director of Research (if dissertation) or Advisor (if thesis)

Chen, Deming

Department of Study

Electrical & Computer Eng

Discipline

Electrical & Computer Engr

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Date of Ingest

2016-11-10T18:35:35Z

Keyword(s)

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

Abstract

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.

Graduation Semester

2016-08

Type of Resource

text

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

Copyright and License Information

Copyright 2016 Yan Yan

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