Using GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows--Wheeler Transform.

TitleUsing GPUs for the Exact Alignment of Short-read Genetic Sequences by Means of the Burrows--Wheeler Transform.
Publication TypeJournal Article
Year of Publication2012
AuthorsSalavert Torres J, Blanquer Espert I, Tomas Dominguez A, Hernendez V, Medina I, Terraga J, Dopazo J
Journal TitleIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM
Volume9
Issue4
Pages1245-1256
Journal Date2012 Mar 20
ISSN1557-9964
KeywordsBurrows-Wheeler transform, CPU execution, GPGPU, NGS
AbstractGeneral 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.
URLhttp://ieeexplore.ieee.org.sire.ub.edu/xpl/articleDetails.jsp?reload=true&arnumber=6175888
DOI10.1109/TCBB.2012.49
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PDF800.45 KB