|Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows–Wheeler Transform.
|Year of Publication
|Torres, JSalavert, Espert, IBlanquer, Dominguez, ATomas, Hernendez, V, Medina, I, Terraga, J, Dopazo, J
|IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM
|2012 Mar 20
|Burrows-Wheeler transform; CPU execution; GPGPU; NGS
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.