FPGA acceleration of short read alignment with high-level synthesis

With the introduction of next-generation sequencing (NGS) technologies, DNA sequencing is becoming an increasingly widespread process. When performed on human patients, it can allow for the prediction and prevention of diseases. An essential part of this bioinformatics pipeline is short read alignment}, which refers to aligning short fragments of DNA to the large and expansive reference genome. This can be a very time-consuming process with much room for improvement. This thesis improves on Bowtie 2, an aligner that is already very popular and high-performing. Through the use of OpenCL, it is possible to parallelize this application for both GPU and FPGA by using the same code. Several different levels of parallelism are implemented in order to achieve speedup on Bowtie 2.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Electrical and Computer Engineering

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2017

Author dc:creator

• Chen, Daniel E

Contributors dc:contributor

• Chen, Deming

• Field-programmable gate array (FPGA)
• Hardware acceleration
• High-level synthesis
• OpenCL
• Short read alignment

Statement dc:rights

• Copyright 2017 Daniel E. Chen

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/97641

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/97641