A DNA Read Alignment Accelerator Based on Computational RAM
A DNA Read Alignment Accelerator Based on Computational RAM
复制标题
DOI：
10.1109/jxcdc.2020.2987527
复制
发表时间：
2020-04
影响因子：
2.4
通讯作者：
Z. Chowdhury;Masoud Zabihi;S. K. Khatamifard;Zhengyang Zhao;Salonik Resch;Meisam Razaviyayn;Jianping Wang;S. Sapatnekar;Ulya R. Karpuzcu
中科院分区：
文献类型：
--
作者：
Z. Chowdhury;Masoud Zabihi;S. K. Khatamifard;Zhengyang Zhao;Salonik Resch;Meisam Razaviyayn;Jianping Wang;S. Sapatnekar;Ulya R. Karpuzcu
近年来，在内存中处理（PIM）的范例在计算中，由于它的承诺，以提高性能，通过减少能量消耗和长延迟的内存访问，见证了越来越多的兴趣。加入爆炸的数据处理，产生的基因组学，特别是基因组测序，PIM已成为一个潜在的有前途的候选人，加速基因组学的应用，因为他们没有规模以及在传统的冯诺依曼系统。在这篇文章中，我们提出了一个内存加速器架构的DNA读对齐。即使在保守的假设下，该架构在吞吐量和能效方面也分别优于相应的软件实现> 49倍和>18 000倍。
Recent years have witnessed an increasing interest in the processing-in-memory (PIM) paradigm in computing due to its promise to improve the performance through the reduction of energy-hungry and long-latency memory accesses. Joined with the explosion of data to be processed, produced in genomics—particularly genome sequencing—PIM has become a potential promising candidate for accelerating genomics applications since they do not scale up well in conventional von Neumann systems. In this article, we present an in-memory accelerator architecture for DNA read alignment. This architecture outperforms corresponding software implementation by >49X and >18 000X, in terms of throughput and energy efficiency, respectively, even under conservative assumptions.