Abstract
The vast increase in DNA sequencing capacity over the last decade has quickly turned biology into a dataintensive science. Nevertheless, current sequencers such as Illumia HiSeq have high random per-base error rates, which makes sequencing error correction an indispensable requirement for many sequence analysis applications. Most existing error correction methods demand large expensive memory space, which limits their scalability for handling large datasets. In this paper, we present a new disk based method, called DiskBQcor, for sequencing error correction. DiskBQcor stores k-mers of sequencing genome data along with their associated metadata on inexpensive disk and utilizes a disk based index tree to efficiently process special box queries to obtain relevant k-mers and their occurring frequencies. It then applies a comprehensive voting mechanism and possibly an efficient binary encoding based assembly technique to verify and correct an erroneous base in a genome sequence under various conditions. Our experiments demonstrate that the proposed method is quite promising in error verification and correction for sequencing genome data on disk.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016 |
| Publisher | The International Society for Computers and Their Applications (ISCA) |
| Pages | 69-76 |
| Number of pages | 8 |
| ISBN (Electronic) | 9781943436033 |
| State | Published - Jan 1 2016 |
| Externally published | Yes |
| Event | 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016 - Las Vegas, United States Duration: Apr 4 2016 → Apr 6 2016 |
Other
| Other | 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016 |
|---|---|
| Country | United States |
| City | Las Vegas |
| Period | 4/4/16 → 4/6/16 |
Fingerprint
Keywords
- Algorithm
- Box query
- DNA sequencing
- Error correction
- Index tree
ASJC Scopus subject areas
- Artificial Intelligence
- Computational Theory and Mathematics
- Information Systems
- Biomedical Engineering
- Electrical and Electronic Engineering
- Health Informatics
Cite this
Using disk based index and box queries for genome sequencing error correction. / Gu, Yarong; Zhu, Qiang; Liu, Xianying; Dong, Youchao; Brown, Charles; Pramanik, Sakti.
Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016. The International Society for Computers and Their Applications (ISCA), 2016. p. 69-76.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Using disk based index and box queries for genome sequencing error correction
AU - Gu, Yarong
AU - Zhu, Qiang
AU - Liu, Xianying
AU - Dong, Youchao
AU - Brown, Charles
AU - Pramanik, Sakti
PY - 2016/1/1
Y1 - 2016/1/1
N2 - The vast increase in DNA sequencing capacity over the last decade has quickly turned biology into a dataintensive science. Nevertheless, current sequencers such as Illumia HiSeq have high random per-base error rates, which makes sequencing error correction an indispensable requirement for many sequence analysis applications. Most existing error correction methods demand large expensive memory space, which limits their scalability for handling large datasets. In this paper, we present a new disk based method, called DiskBQcor, for sequencing error correction. DiskBQcor stores k-mers of sequencing genome data along with their associated metadata on inexpensive disk and utilizes a disk based index tree to efficiently process special box queries to obtain relevant k-mers and their occurring frequencies. It then applies a comprehensive voting mechanism and possibly an efficient binary encoding based assembly technique to verify and correct an erroneous base in a genome sequence under various conditions. Our experiments demonstrate that the proposed method is quite promising in error verification and correction for sequencing genome data on disk.
AB - The vast increase in DNA sequencing capacity over the last decade has quickly turned biology into a dataintensive science. Nevertheless, current sequencers such as Illumia HiSeq have high random per-base error rates, which makes sequencing error correction an indispensable requirement for many sequence analysis applications. Most existing error correction methods demand large expensive memory space, which limits their scalability for handling large datasets. In this paper, we present a new disk based method, called DiskBQcor, for sequencing error correction. DiskBQcor stores k-mers of sequencing genome data along with their associated metadata on inexpensive disk and utilizes a disk based index tree to efficiently process special box queries to obtain relevant k-mers and their occurring frequencies. It then applies a comprehensive voting mechanism and possibly an efficient binary encoding based assembly technique to verify and correct an erroneous base in a genome sequence under various conditions. Our experiments demonstrate that the proposed method is quite promising in error verification and correction for sequencing genome data on disk.
KW - Algorithm
KW - Box query
KW - DNA sequencing
KW - Error correction
KW - Index tree
UR - http://www.scopus.com/inward/record.url?scp=84973641934&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84973641934&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:84973641934
SP - 69
EP - 76
BT - Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016
PB - The International Society for Computers and Their Applications (ISCA)
ER -