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.

中文翻译：

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序列对齐的 FPGA 加速：调查

基因组学正在改变我们对人类、进化、疾病和药物的理解，仅举几例。随着测序技术的发展，收集 DNA 序列所需的时间更少，从而每天产生更多的基因数据。今天，生成基因数据的速度超过了计算能力的增长速度。目前的测序机每天可以对 50 个人类基因组进行测序；然而，将读取序列与参考基因组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数与参考基因组对齐。已经提出了许多加速器来加速 DNA 对齐过程。基于 FPGA 的加速器提供大规模并行性，在加速 DNA 对齐算法方面表现出出色的性能。此外，基于 FPGA 的加速器提供比通用处理器更好的能效。在本次调查中，我们介绍了三种主要的 DNA 对齐算法和这些算法的基于 FPGA 的实现，以加速 DNA 对齐。我们还比较了这三个对齐类别，并展示了加速器在此期间的发展情况。