|Title||Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows--Wheeler Transform. |
|Publication Type||Journal Article |
|Year of Publication||2012 |
|Authors||Salavert Torres J, Blanquer Espert I, Tomas Dominguez A, Hernendez V, Medina I, Terraga J, Dopazo J |
|Journal Title||IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM |
|Journal Date||2012 Mar 20 |
|Keywords||Burrows-Wheeler transform, CPU execution, GPGPU, NGS |
|Abstract||General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm with state-of-the-art implementations of the same algorithm over standard CPUs, and considering the same conditions in terms of I/O. Excluding disk transfers, the implementation of the algorithm in GPUs shows a speedup larger than 12x, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximising memory locality and ensuring a symmetric access to the data. The article describes the behaviour of the algorithm in GPU, showing a good scalability in the performance, only limited by the size of the GPU inner memory.