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
Keyword(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.
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