A Literature Evaluation of CUDA Compatible Sequence Aligners

Yang Liu, Jiang-Yu Li, Yi-Qing Mao, Xiao-Lei Wang, Dong-Sheng Zhao

2013

Abstract

The rapidly accumulating biological data generated by next-generation sequencer motivate the development of improved tools for sequence alignment. Many technologies have been proposed for this purpose, and one of them is GPU computing. Existing acceleration of sequence aligners using GPU computing overemphasize speed. However, other factors such as accuracy, performance per watt, price-performance and programming complexity are also important and need to be considered. Based on the existing literatures of GPU-based sequence aligners, this paper gives a literature evaluation of these sequence aligners from the above perspectives, in order to determine the usability of the tremendous GPU-based sequence aligners.

References

  1. Amazon, [online], Available: http://www.amazon.com Accessed 2012-07-12.
  2. AMD official website, [online], Available: http://products. amd.com/pages/opteroncpuresult.aspx?AspxAutoDete ctCookieSupport=1 Accessed 2012-10-20.
  3. Edgar, R. C., 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, vol. 26, no. 19, pp. 2460-2461.
  4. Geeks3d, [online], Available: http://www.geeks3d.com/20 090618/graphics-cards-thermal-design-power-tdp-data base Accessed 2012-07-12.
  5. Intel official website, [online], Available: http://ark.intel.c om Accessed 2012-10-20.
  6. Klus, P., Lam, S., Lyberg, D., Cheung, M. S., Pullan, G., McFarlane, I., Yeo, G., Lam, B., 2012. BarraCUDA - a fast short read sequence aligner using graphics processing units. BMC Research Notes, vol. 5, no. 1, pp. 27.
  7. Liu, Y., Maskell, D. L., Schmidt, B., 2009. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res Notes, vol. 2, pp. 73.
  8. Liu, W., Schmidt, B., Muller-Wittig, W., 2011. CUDABLASTP: accelerating BLASTP on CUDA-enabled graphics hardware. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 8, no. 6, pp. 1678-1684.
  9. Liu, C. M., Wong, T., Wu, E., Luo, R., Yiu, S. M., Li, Y., Wang, B., Yu, C., Chu, X., Zhao, K., Li, R., Lam, T. W., 2012. SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, doi: 10.1093/bioinformatics/bts061.
  10. Manavski, S. A., Valle, G., 2008. CUDA compatible GPU cards as efficient hardware accelerators for SmithWaterman sequence alignment. BMC Bioinformatics, vol. 9, no. Suppl 2, pp. S10.
  11. Nvidia Tesla, [online], Available: http://en.wikipedia.org/ wiki/Nvidia_Tesla Accessed 2012-07-12.
  12. OpenACC, [online], Available: http://www.openacc-stand ard.org Accessed 2012-07-12.
  13. OpenHMPP, [online], Available: http://www.openhmpp.or g Accessed 2012-07-12.
  14. Schatz, M. C., Trapnell, C., Delcher, A. L., Varshney, A., 2007. High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics, vol. 8, pp. 474.
  15. Sequence alignment software, [online], Available: http://en.wikipedia.org/wiki/List_of_sequence_alignm ent_software Accessed 2012-07-12.
  16. Striemer, G. M., Akoglu, A., 2009. Sequence Alignment with GPU: Performance and Design Challenges. In IEEE International Symposium on Parallel and Distributed Processing.
  17. Vouzis, P. D., Sahinidis, N. V., 2011. GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics, vol. 27, no. 2, pp. 182-188.
  18. Walters, J. P., Balu, V., Kompalli, S., Chaudhary, V., 2008. Evaluating the use of GPUs for life science applications. Buffalo, NY: The State University of New York, http://www.cse.buffalo.edu/techreports/2008-10.pdf. Accessed 2012-03-19.
  19. Tweakers, [online], Available: http://tweakers.net/pricewat ch Accessed 2012-10-20.
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Paper Citation


in Harvard Style

Liu Y., Li J., Mao Y., Wang X. and Zhao D. (2013). A Literature Evaluation of CUDA Compatible Sequence Aligners . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 268-271. DOI: 10.5220/0004191202680271


in Bibtex Style

@conference{bioinformatics13,
author={Yang Liu and Jiang-Yu Li and Yi-Qing Mao and Xiao-Lei Wang and Dong-Sheng Zhao},
title={A Literature Evaluation of CUDA Compatible Sequence Aligners },
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={268-271},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004191202680271},
isbn={978-989-8565-35-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - A Literature Evaluation of CUDA Compatible Sequence Aligners
SN - 978-989-8565-35-8
AU - Liu Y.
AU - Li J.
AU - Mao Y.
AU - Wang X.
AU - Zhao D.
PY - 2013
SP - 268
EP - 271
DO - 10.5220/0004191202680271