PSI-RA: A parallel sparse index for read alignment on genomes
Document Type
Conference Proceeding
Publication Date
12-1-2010
Abstract
We concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named PSI-RA (parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to tune the space consumption of the index based on the available memory of the machine and the minimum length of the arriving pattern queries. Although SSAs have been studied before on exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the right-most mismatch criteria that prioritizes the errors towards the end of the reads since it is known that the errors are more probable at that area. PSI-RA supports any number of mismatches in aligning reads. We give comparisons with some of the well known short read aligners, and show that indexing genome with SSA is a good alternative to Burrows-Wheeler transform or seed based solutions. ©2010 IEEE.
Publication Source (Journal or Book title)
Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
First Page
663
Last Page
668
Recommended Citation
Külekci, M., Hon, W., Shah, R., Vitter, J., & Xu, B. (2010). PSI-RA: A parallel sparse index for read alignment on genomes. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, 663-668. https://doi.org/10.1109/BIBM.2010.5706648
