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dc.contributor.authorKulekci, M. Oguzhan
dc.contributor.authorHon, Wing-Kai
dc.contributor.authorShah, Rahul
dc.contributor.authorVitter, Jeffrey Scott
dc.contributor.authorXu, Bojian
dc.identifier.citationKülekci, M. Oğuzhan, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter, and Bojian Xu. "Ψ-RA: A Parallel Sparse Index for Genomic Read Alignment." BMC Genomics 12.Suppl 2 (2011).
dc.descriptionThis is the published version. Copyright © 2011 Oğuzhan Külekci et al; licensee BioMed Central Ltd.en_US

Genomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same species share the majority of their genomes, short reads alignment provides an alternative and much more efficient way to sequence the genome of a particular individual than does direct sequencing. Among many strategies proposed for this alignment process, indexing the reference genome and short read searching over the index is a dominant technique. Our goal is to design a space-efficient indexing structure with fast searching capability to catch the massive short reads produced by the next generation high-throughput DNA sequencing technology. Results

We concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named Ψ-RA (PSI-RA: parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to fine 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 for exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the rightmost mismatch criteria that prioritize the errors towards the end of the reads, where errors are more probable. Ψ-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 a genome with SSA is a good alternative to the Burrows-Wheeler transform or seed-based solutions. Conclusions

Ψ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology. Ψ-RA is very fast in exact matching and also supports rightmost approximate matching. The SSA structure that Ψ-RA is built on naturally incorporates the modern multicore architecture and thus further speed-up can be gained. All the information, including the source code of Ψ-RA, can be downloaded at: webcite.
dc.publisherBioMed Centralen_US
dc.titleΨ-RA: a parallel sparse index for genomic read alignmenten_US
kusw.kuauthorVitter, Jeffrey
kusw.kudepartmentElectrical Engr & Comp Scienceen_US
kusw.oaversionScholarly/refereed, publisher version
kusw.oapolicyThis item meets KU Open Access policy criteria.

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