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Title:FPGA acceleration of DNA error correction
Author(s):Ramachandran, Anand
Advisor(s):Chen, Deming
Department / Program:Electrical & Computer Eng
Discipline:Electrical & Computer Engr
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:M.S.
Genre:Thesis
Subject(s):Field programmable gate arrays (FPGA)
Acceleration
Sequencing
DNA error correction
Abstract: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.
Issue Date:2016-12-05
Type:Thesis
URI:http://hdl.handle.net/2142/95394
Rights Information:Copyright 2016 Anand Ramachandran
Date Available in IDEALS:2017-03-01
Date Deposited:2016-12


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