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 |
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Keywords
- Bloom filter
- DNA
- error correction
- FPGA
ASJC Scopus subject areas
- Engineering(all)
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
}
TY - GEN
T1 - FPGA accelerated DNA error correction
AU - Ramachandran, Anand
AU - Heo, Yun
AU - Hwu, Wen-Mei W
AU - Ma, Jian
AU - Chen, Deming
PY - 2015/4/22
Y1 - 2015/4/22
N2 - 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.
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.
KW - Bloom filter
KW - DNA
KW - error correction
KW - FPGA
UR - http://www.scopus.com/inward/record.url?scp=84945916935&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84945916935&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:84945916935
VL - 2015-April
SP - 1371
EP - 1376
BT - Proceedings of the 2015 Design, Automation and Test in Europe Conference and Exhibition, DATE 2015
PB - Institute of Electrical and Electronics Engineers Inc.
ER -