Trapnell, C., Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35 (8-9). pp. 429-440. ISSN 01678191 (ISSN)
Abstract
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease genotyping and personal genomics. MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13× faster than the serial CPU version of the alignment code and nearly 4× faster in total computation time than MUMmerGPU 1.0. We exhaustively examined 128 GPU data layout configurations to improve register footprint and running time and conclude higher occupancy has greater impact than reduced latency. MUMmerGPU is available open-source at http://www.mummergpu.sourceforge.net. © 2009 Elsevier B.V. All rights reserved.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | CUDA GPGPU Short read mapping Suffix trees Data intensive Data layouts Data-intensive computation Depth first search Diverse applications DNA sequence data Genomics Genotyping Graphics Processing Unit Open-source Running time Total computation time Alignment Computer graphics equipment DNA Genes Nucleic acids Program processors |
| Subjects: | bioinformatics > genomics and proteomics > analysis and processing bioinformatics > genomics and proteomics > alignment > sequence alignment bioinformatics > genomics and proteomics > annotation > sequence annotation bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering bioinformatics > computational biology bioinformatics > genomics and proteomics > computers > computer software Investigative techniques and equipment > interface method |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | CSHL Librarian |
| Date: | 2009 |
| Date Deposited: | 16 Mar 2012 14:39 |
| Last Modified: | 15 Mar 2013 19:12 |
| PMCID: | PMC2749273 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/25362 |
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