This article presents the first dedicated system-on-chip (SoC) that supports full data analysis workflow for genetic variant discovery for next-generation sequencing (NGS). The SoC implements four major steps: preprocessing, short-read mapping, haplotype calling, and variant calling. By adopting the sBWT-based short read mapping and Genome Analysis ToolKit haplotype caller-based variant calling algorithms, this work achieves a comparable precision as the software solutions. The dedicated hardware architecture achieves high parallelism with low hardware complexity. In this SoC, the multitask sorting engine and the dynamic programming processing engine are proposed for essential computing tasks for NGS data analysis. An ARC processor is integrated to facilitate IO interfaces, including a DDR3 PHY. Fabricated in a 28-nm technology, the chip area is 12 mm². It dissipates 975 mW at a clock frequency of 400 MHz from a 0.9-V supply. The SoC is able to complete variant discovery for the whole human genome within 37 min. Compared with an optimized graphic processing unit solution, this work is 66 $\times $ faster and also achieves an $1.59\times 10^{4}$ times higher energy efficiency and 3086 $\times $ higher area efficiency. Verified with the FDA standardized benchmark, the SoC achieves a precision of 99.6%. The prototype system demonstrates the analysis procedure in real time for on-site DNA sequencing.

中文翻译：

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用于下一代测序的 975 mW 28 nm 全集成遗传变异发现片上系统

本文介绍了首款支持用于下一代测序 (NGS) 遗传变异发现的完整数据分析工作流程的专用片上系统 (SoC)。SoC 实现四个主要步骤：预处理、短读映射、单倍型调用和变体调用。通过采用基于 sBWT 的短读映射和基因组分析工具包基于单体型调用者的变异调用算法，这项工作实现了与软件解决方案相当的精度。专用硬件架构以低硬件复杂度实现了高并行度。在该 SoC 中，针对 NGS 数据分析的基本计算任务，提出了多任务排序引擎和动态编程处理引擎。集成了 ARC 处理器以促进 IO 接口，包括 DDR3 PHY。采用 28 纳米技术制造，² . 它在 400 MHz 时钟频率下从 0.9 V 电源消耗 975 mW。SoC 能够在 37 分钟内完成整个人类基因组的变异发现。与优化的图形处理单元解决方案相比，这项工作是 66 $\times $ 更快，还实现了 $1.59\乘以 10^{4}$ 能效提高 3086 倍 $\times $ 更高的区域效率。通过 FDA 标准化基准验证，SoC 实现了 99.6% 的精度。原型系统实时演示现场 DNA 测序的分析过程。