FPGA accelerated DNA error correction

Anand Ramachandran; Yun Heo; Wen-Mei W Hwu; Jian Ma; Deming Chen

FPGA accelerated DNA error correction

Anand Ramachandran, Yun Heo, Wen-Mei W Hwu, Jian Ma, Deming Chen

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analysis 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 current paper describes the first FPGA-based error-correction tool, called FPGA Accelerated DNA Error Correction (FADE), which targets to improve the throughput of DNA error correction for Illumina reads. The base algorithm of FADE is BLESS that is highly accurate but slow. A Bloom filter that is the main data structure of BLESS and BLESS' error correction subroutines for different types of errors have been implemented on a FPGA. We compared our design with the software version of BLESS using DNA sequencing data generated from four genomes and we could achieve up to 43 times speedup for the best case, and 36 times speedup on the average.

Original language	English (US)
Title of host publication	Proceedings of the 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1371-1376
Number of pages	6
Volume	2015-April
ISBN (Electronic)	9783981537048
State	Published - Apr 22 2015
Event	2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015 - Grenoble, France Duration: Mar 9 2015 → Mar 13 2015

Other

Other	2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015
Country	France
City	Grenoble
Period	3/9/15 → 3/13/15

Keywords

Bloom filter
DNA
error correction
FPGA

ASJC Scopus subject areas

Engineering(all)

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Cite this

FPGA accelerated DNA error correction. / Ramachandran, Anand; Heo, Yun; Hwu, Wen-Mei W; Ma, Jian; Chen, Deming.

Proceedings of the 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015. Vol. 2015-April Institute of Electrical and Electronics Engineers Inc., 2015. p. 1371-1376 7092605.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Ramachandran, A, Heo, Y, Hwu, W-MW, Ma, J & Chen, D 2015, FPGA accelerated DNA error correction. in Proceedings of the 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015. vol. 2015-April, 7092605, Institute of Electrical and Electronics Engineers Inc., pp. 1371-1376, 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015, Grenoble, France, 3/9/15.

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AB - Correcting errors in DNA sequencing data is an important process that can improve the quality of downstream analysis 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 current paper describes the first FPGA-based error-correction tool, called FPGA Accelerated DNA Error Correction (FADE), which targets to improve the throughput of DNA error correction for Illumina reads. The base algorithm of FADE is BLESS that is highly accurate but slow. A Bloom filter that is the main data structure of BLESS and BLESS' error correction subroutines for different types of errors have been implemented on a FPGA. We compared our design with the software version of BLESS using DNA sequencing data generated from four genomes and we could achieve up to 43 times speedup for the best case, and 36 times speedup on the average.

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