Succincter text indexing with wildcards
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
ERA: efficient serial and parallel suffix tree construction for very long strings
Proceedings of the VLDB Endowment
Detection of novel tandem duplication with next-generation sequencing
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Bidirectional search in a string with wavelet trees and bidirectional matching statistics
Information and Computation
Integrating GPU-accelerated sequence alignment and SNP detection for genome resequencing analysis
SSDBM'12 Proceedings of the 24th international conference on Scientific and Statistical Database Management
Computing the burrows-wheeler transform of a string and its reverse
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
High-performance short sequence alignment with GPU acceleration
Distributed and Parallel Databases
Computing the longest common prefix array based on the Burrows-Wheeler transform
Journal of Discrete Algorithms
Hardware acceleration of genetic sequence alignment
ARC'13 Proceedings of the 9th international conference on Reconfigurable Computing: architectures, tools, and applications
Compressed indexes for text with wildcards
Theoretical Computer Science
Multi-pattern matching with bidirectional indexes
Journal of Discrete Algorithms
Computing the Burrows-Wheeler transform of a string and its reverse in parallel
Journal of Discrete Algorithms
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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.