论文标题
序列对齐的FPGA加速度：调查
FPGA Acceleration of Sequence Alignment: A Survey
论文作者
论文摘要
基因组学正在改变我们对人类，进化，疾病和药物的理解，但要列举一些。随着测序技术的开发，收集DNA序列的时间更少，从而每天生成更多的遗传数据。如今，产生遗传数据的速度超过了计算功率增长率。当前的测序机每天可以对50人类的基因组进行序列。但是，将读取序列与参考基因组进行对齐并组装基因组将需要1300个CPU小时。构建基因组的主要步骤是将读取与参考基因组对齐。已经提出了许多加速器来加速DNA对准过程。提供大量的并行性，基于FPGA的加速器在加速DNA比对算法方面表现出色。此外，基于FPGA的加速器比通用处理器提供更好的能效率。在这项调查中，我们介绍了这些算法的三种主要DNA比对算法和基于FPGA的实现，以加速DNA对齐。我们还比较了这三个对齐类别，并展示了当时加速器的发展方式。
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the rate of generating genetic data is outpacing the rate of computation power growth. Current sequencing machines can sequence 50 humans genome per day; however, aligning the read sequences against a reference genome and assembling the genome will take 1300 CPU hours. The main step in constructing the genome is aligning the reads against a reference genome. Numerous accelerators have been proposed to accelerate the DNA alignment process. Providing massive parallelism, FPGA-based accelerators have shown great performance in accelerating DNA alignment algorithms. Additionally, FPGA-based accelerators provide better energy efficiency than general-purpose processors. In this survey, we introduce three main DNA alignment algorithms and FPGA-based implementation of these algorithms to accelerate the DNA alignment. We also, compare these three alignment categories and show how accelerators are developing during the time.
