Benchmarking BarraCUDA on Epigenetic DNA and nVidia Pascal GPUs

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Langdon, W;
  • Related identifiers: doi: 10.1101/095075
  • Subject: bepress|Life Sciences|Biology | bepress|Life Sciences|Bioinformatics

Typically BarraCUDA uses CUDA graphics cards to map DNA reads to the human genome. Previously its software source code was genetically improved for short paired end next generation sequences. On longer, 150 base paired end noisy Cambridge Epigenetix's data, a Pascal GTX... View more
  • References (7)

    [1] P. Klus, S. Lam, D. Lyberg, M. S. Cheung, G. Pullan, I. McFarlane, G. S. H. Yeo, and Brian Y. H. Lam. BarraCUDA - a fast short read sequence aligner using graphics processing units. BMC Research Notes, 5(27), 2012.

    [2] W. B. Langdon. Genetically improved software. In A. H. Gandomi et al., editors, Handbook of Genetic Programming Applications, chapter 8, pages 181-220. Springer, 2015.

    [3] W. B. Langdon. Computational biology in the 21st century is parallel. Communications of the ACM, 59(11):9, November 2016. Letter to the editor.

    [4] W. B. Langdon and Brian Y. H. Lam. Genetically improved BarraCUDA. Research Note RN/15/03, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK, 28 May 2015.

    [5] W. B. Langdon, Brian Y. H. Lam, J. Petke, and M. Harman. Improving CUDA DNA analysis software with genetic programming. In S. Silva et al., editors, GECCO, pages 1063-1070, Madrid, 11-15 July 2015. ACM.

    [6] W. B. Langdon, A. Vilella, Brian Y. H. Lam, J. Petke, and M. Harman. Benchmarking genetically improved BarraCUDA on epigenetic methylation NGS datasets and nVidia GPUs. In J. Petke et al., editors, Genetic Improvement 2016 Workshop, pages 1131-1132, Denver, July 20-24 2016. ACM.

    [7] J. D. Owens, M. Houston, D. Luebke, S. Green, J. E. Stone, and J. C. Phillips. GPU computing. Proceedings of the IEEE, 96(5):879-899, May 2008. Invited paper.

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