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Authors: Yang Liu ; Jiang-Yu Li ; Yi-Qing Mao ; Xiao-Lei Wang and Dong-Sheng Zhao

Affiliation: Academy of Military Medical Sciences, China

Keyword(s): CUDA, Sequence Aligner, Performance per Watt, Price-performance, Programming Complexity

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis

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.

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Paper citation in several formats:
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 (BIOSTEC 2013) - BIOINFORMATICS; ISBN 978-989-8565-35-8; ISSN 2184-4305, SciTePress, pages 268-271. DOI: 10.5220/0004191202680271

@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 (BIOSTEC 2013) - BIOINFORMATICS},
year={2013},
pages={268-271},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004191202680271},
isbn={978-989-8565-35-8},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2013) - BIOINFORMATICS
TI - A Literature Evaluation of CUDA Compatible Sequence Aligners
SN - 978-989-8565-35-8
IS - 2184-4305
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
PB - SciTePress

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