DNA变异调用的Pair-HMM算法加速

2016 IEEE 24th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) Pub Date : 2016-05-01 DOI:10.1145/3020078.3021749

Sitao Huang, G. Manikandan, Anand Ramachandran, K. Rupnow, Wen-mei W. Hwu, Deming Chen

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引用次数: 46

摘要

在这个项目中，我们提出了一个SoC解决方案来加速Pair-HMM的前向算法，这是GATK的HaplotypeCaller工具用于DNA变异调用的关键性能瓶颈。我们开发了两个版本的Pair-HMM加速器:一个使用高级合成(HLS)，另一个基于环的手动RTL实现。我们在设计灵活性和总体运行时间方面研究了手动RTL设计和HLS设计的性能。我们通过HLS实现实现了高达19倍的显著加速，通过RTL实现的算法实现了高达95倍的加速。

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Acceleration of the Pair-HMM Algorithm for DNA Variant Calling

In this project, we propose an SoC solution to accelerate the Pair-HMM's forward algorithm which is the key performance bottleneck in the GATK's HaplotypeCaller tool for DNA variant calling. We develop two versions of the Pair-HMM accelerator: one using High Level Synthesis (HLS), and another ring-based manual RTL implementation. We investigate the performance of the manual RTL design and HLS design in terms of design flexibility and overall run-time. We achieve a significant speed-up of up to 19x through the HLS implementation and speed-up of up to 95x through the RTL implementation of the algorithm.

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来源期刊

2016 IEEE 24th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM)

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