DNA变异召唤的带状对hmm算法及其硬件加速器设计

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI:10.1109/BIBE.2019.00107

Ming-Hung Chen, Mao-Jan Lin, Yu-Cheng Li, Yi-Chang Lu

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引用次数: 1

摘要

本文提出了一种新的对隐马尔可夫模型(pair - hmm)算法，即带状对隐马尔可夫算法，它是一种针对变量调用应用的启发式方法。与传统的Pair-HMM相比，我们的带状Pair-HMM可以在较小的精度成本下减少执行时间。在此基础上，采用台积电40nm工艺实现了硬件加速器。正如本文后面所展示的，所提出的硬件加速器比传统的Pair-HMM硬件快4倍，比原始的Pair-HMM软件快17000倍以上。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Banded Pair-HMM Algorithm for DNA Variant Calling and Its Hardware Accelerator Design

In this paper, we propose a new pair hidden Markov model (Pair-HMM) algorithm, namely Banded Pair-HMM, which is a heuristic approach for variant calling applications. When compared to the conventional Pair-HMM, our Banded Pair-HMM can reduce the execution time at a minor cost in accuracy. In addition, a hardware accelerator is implemented using TSMC 40nm technology based on the proposed algorithm. As demonstrated later in the paper, the proposed hardware accelerator runs 4× faster than the conventional Pair-HMM hardware, and over 17,000× faster than the original Pair-HMM software.

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2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)

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