论文标题
加速基因组分析：正在进行的旅程中的入门
Accelerating Genome Analysis: A Primer on an Ongoing Journey
论文作者
论文摘要
基因组分析从根本上讲是从称为读图的过程开始的，在该过程中，将生物体基因组的测序片段与参考基因组进行了比较。当前，读取映射是整个基因组分析管道中的主要瓶颈，因为最先进的基因组测序技术能够比用于分析基因组的计算技术更快地对基因组进行测序。我们描述了正在进行的旅程，以显着提高阅读映射的性能。我们解释了最先进的算法方法和基于硬件的加速方法。算法方法利用基因组的结构以及基础硬件的结构。基于硬件的加速方法利用专业的微体系结构或各种执行范例（例如，内存内或附近的处理）。我们最终面临采用这些硬件加速读取映射器的挑战。
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are able to sequence a genome much faster than the computational techniques employed to analyze the genome. We describe the ongoing journey in significantly improving the performance of read mapping. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory). We conclude with the challenges of adopting these hardware-accelerated read mappers.
