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.

中文翻译：

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加速基因组分析：持续旅程的入门指南


基因组分析从根本上开始于称为读取映射的过程，其中将生物体基因组的测序片段与参考基因组进行比较。读取映射目前是整个基因组分析流程中的主要瓶颈，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。我们描述了显着提高读取映射性能的持续历程。我们解释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底层硬件的结构。基于硬件的加速方法利用专门的微架构或各种执行范例（例如，在内存内或内存附近进行处理）。我们最后总结了采用这些硬件加速读取映射器的挑战。