FPGA acceleration of DNA error correction

Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analyses using the data. Even though many error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base algorithm of the FPGA implementation is BLESS which is highly accurate but slow. The hardware implemented on the FPGA consists of a Bloom filter that is the main data structure of BLESS and the error-correction subroutines in BLESS. The design is compared with the software version of BLESS, and two other leading tools. The results show significant improvements in speed for the FPGA-based implementation with comparable accuracy of error correction.

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

2017

Author dc:creator

• Ramachandran, Anand

Contributors dc:contributor

• Chen, Deming

• Field programmable gate arrays (FPGA)
• Acceleration
• Sequencing
• DNA error correction

Statement dc:rights

• Copyright 2016 Anand Ramachandran

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/95394

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/95394