FPGA accelerated DNA error correction

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

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish (US)
Title of host publicationProceedings of the 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1371-1376
Number of pages6
Volume2015-April
ISBN (Electronic)9783981537048
StatePublished - Apr 22 2015
Event2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015 - Grenoble, France
Duration: Mar 9 2015Mar 13 2015

Other

Other2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015
CountryFrance
CityGrenoble
Period3/9/153/13/15

Fingerprint

Error correction
Field programmable gate arrays (FPGA)
DNA
Genes
Throughput
Subroutines
Data structures

Keywords

  • Bloom filter
  • DNA
  • error correction
  • FPGA

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Ramachandran, A., Heo, Y., Hwu, W-M. W., 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, pp. 1371-1376). [7092605] Institute of Electrical and Electronics Engineers Inc..

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 proceedingConference 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.
Ramachandran A, Heo Y, Hwu W-MW, Ma J, Chen D. FPGA accelerated DNA error correction. In 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
Ramachandran, Anand ; Heo, Yun ; Hwu, Wen-Mei W ; Ma, Jian ; Chen, Deming. / FPGA accelerated DNA error correction. 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. pp. 1371-1376
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