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CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
School of Computer Engineering, Nanyang Technological University, Singapore 639798
Bioinformatics, 2012

@article{liu2012cushaw,

   title={CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform},

   author={Liu, Y. and Schmidt, B. and Maskell, D.L.},

   journal={Bioinformatics},

   year={2012},

   publisher={Oxford Univ Press}

}

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Motivation: New high-throughput sequencing technologies have promoted the production of short reads with dramatically low unit cost. The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed. Results: We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphics hardware as accelerators to achieve fast speed. Our algorithm employs a quality-aware bounded search approach based on the Burrows- Wheeler transform (BWT) and the Ferragina Manzini (FM)-index to reduce the search space and achieve high alignment quality. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units (GPUs) achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments compared to three popular BWT-based aligners: Bowtie, BWA and SOAP2. CUSHAW also delivers competitive performance in terms of SNP calling for an E.coli test dataset. Availability: http://cushaw.sourceforge.net.
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