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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing
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A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing

机译：下一代测序中执行读取比对的软件和硬件方法概述

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摘要

Computational genomics is an emerging field that is enabling us to reveal the origins of life and the genetic basis of diseases such as cancer. Next Generation Sequencing (NGS) technologies have unleashed a wealth of genomic information by producing immense amounts of raw data. Before any functional analysis can be applied to this data, read alignment is applied to find the genomic coordinates of the produced sequences. Alignment algorithms have evolved rapidly with the advancement in sequencing technology, striving to achieve biological accuracy at the expense of increasing space and time complexities. Hardware approaches have been proposed to accelerate the computational bottlenecks created by the alignment process. Although several hardware approaches have achieved remarkable speedups, most have overlooked important biological features, which have hampered their widespread adoption by the genomics community. In this paper, we provide a brief biological introduction to genomics and NGS. We discuss the most popular next generation read alignment tools and algorithms. Furthermore, we provide a comprehensive survey of the hardware implementations used to accelerate these algorithms.
机译：计算基因组学是一个新兴领域，使我们能够揭示生命的起源以及诸如癌症等疾病的遗传基础。下一代测序（NGS）技术通过产生大量原始数据释放了丰富的基因组信息。在将任何功能分析应用于该数据之前，应应用读取比对以找到产生的序列的基因组坐标。比对算法随着测序技术的发展而迅速发展，以增加空间和时间复杂度为代价，努力实现生物学准确性。已经提出了硬件方法来加速由对准过程产生的计算瓶颈。尽管几种硬件方法已实现了显着的加速，但大多数方法却忽略了重要的生物学特性，从而阻碍了它们在基因组学领域的广泛采用。在本文中，我们对基因组学和NGS进行了简要的生物学介绍。我们讨论最流行的下一代读取对齐工具和算法。此外，我们提供了用于加速这些算法的硬件实现的全面调查。

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