A Review of Hardware Acceleration for Computational Genomics
A Review of Hardware Acceleration for Computational Genomics
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DOI：
10.1109/mdat.2013.2293757
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发表时间：
2014-01-01
影响因子：
2
通讯作者：
Jammula, Nagakishore
中科院分区：
文献类型：
--
作者：
Aluru, Srinivas;Jammula, Nagakishore
硬件加速器在以传统超级计算机和独立CPU集群的一小部分成本提供高性能计算解决方案方面变得越来越普遍，尽管利用它们需要额外的编程工作。本文提供了一个调查的使用硬件加速器，如FPGA和GPU在生物序列分析领域，特别是在计算基因组学领域。我们还调查了硬件加速的研究，以应对高通量测序的新趋势，以及由此带来的应用。我们总结了这些趋势如何影响生物信息学中硬件加速的使用，以及最近开发或即将发布的加速器技术的作用。
Hardware accelerators are becoming increasingly commonplace in delivering high performance computing solutions at a fraction of the cost of conventional supercomputers and standalone CPU clusters, despite the additional programming effort required to utilize them. This paper provides a survey on the use of hardware accelerators such as FPGAs and GPUs in the area of biological sequence analysis, particularly in the domain of computational genomics. We also survey research on hardware acceleration in response to emerging trends in high-throughput sequencing, and applications enabled by it. We conclude the survey with remarks on how these trends influence the use of hardware acceleration in bioinformatics, and the role of recently developed or soon to be released accelerator technologies.