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2009 IEEE International Conference on Bioinformatics and Biomedicine
High Throughput Short Read Alignment via Bi-directional BWT
Washington, D.C., USA
November 01-November 04
ISBN: 978-0-7695-3885-3
ASCII Text
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T. W. Lam, Ruiqiang Li, Alan Tam, Simon Wong, Edward Wu, S. M. Yiu, "High Throughput Short Read Alignment via Bi-directional BWT," Bioinformatics and Biomedicine, IEEE International Conference on, pp. 31-36, 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009.
 
 
BibTex
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@article{ 10.1109/BIBM.2009.42,
author = {T. W. Lam and Ruiqiang Li and Alan Tam and Simon Wong and Edward Wu and S. M. Yiu},
title = {High Throughput Short Read Alignment via Bi-directional BWT},
journal ={Bioinformatics and Biomedicine, IEEE International Conference on},
volume = {0},
year = {2009},
isbn = {978-0-7695-3885-3},
pages = {31-36},
doi = {http://doi.ieeecomputersociety.org/10.1109/BIBM.2009.42},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
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TY - CONF
JO - Bioinformatics and Biomedicine, IEEE International Conference on
TI - High Throughput Short Read Alignment via Bi-directional BWT
SN - 978-0-7695-3885-3
SP31
EP36
A1 - T. W. Lam,
A1 - Ruiqiang Li,
A1 - Alan Tam,
A1 - Simon Wong,
A1 - Edward Wu,
A1 - S. M. Yiu,
PY - 2009
KW - short read alignment
KW - BWT
KW - indexing data structure
VL - 0
JA - Bioinformatics and Biomedicine, IEEE International Conference on
ER -
 
The advancement of sequencing technologies has made it feasible for researchers to consider many high-throughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of pressure of faster software for alignment. Based on existing indexing and pattern matching technologies, several short read alignment software have been developed recently. Yet this is still strong need to further improve the speed. In this paper, we show a new indexing data structure called bi-directional BWT, which allows us to build the fastest software for aligning short reads. When compared with existing software (Bowtie is the best), our software is at least 3 times faster for finding unique best alignments, and 25 times faster for finding all possible alignments. We believe that bi-directional BWTis an interesting data structure on its own and couldbe applied to other pattern matching problems.
Index Terms:
short read alignment, BWT, indexing data structure
Citation:
T. W. Lam, Ruiqiang Li, Alan Tam, Simon Wong, Edward Wu, S. M. Yiu, "High Throughput Short Read Alignment via Bi-directional BWT," bibm, pp.31-36, 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009
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