Chun-Shen Liu, Nae-Chyun Chen, Yu-Cheng Li, Yi-Chang Lu
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引用次数: 0
摘要
新一代测序技术以其高效的短链测序技术在生物学和医学研究中得到了广泛的应用。de novo sequence assembly在众多应用中,de novo sequence assembly是一种利用NGS短reads获得无参考全基因组的技术。为了使装配结果准确,通常的做法是在装配管道的早期阶段过滤掉低质量的数据。由于滤波占用了大量的装配时间,如何提高滤波阶段的处理速度成为一个重要的问题,特别是在最近的应用中,随着数据规模的增长。在本文中,我们提出了一种基于fpga的高质量滤波器来加快滤波步骤。通过引入One-Hot-encoded蓄电池和相关模块,硬件滤波器可以减少处理时间减半。
An FPGA-based quality filter for de novo sequence assembly pipeline
Next-generation sequencing (NGS) has been widely applied to biological and medical researches for its efficient production of DNA short reads nowadays. Among various applications, de novo sequence assembly is a technique using NGS short reads to obtain a whole genome with no reference. To make assembly results accurate, it is a common practice to filter out low-quality data at the early stage of the assembly pipeline. Since filtering takes a great portion of assembly time, how to increase the processing speed of filtering stage becomes an important issue, especially with growing data scale in recent applications. In this paper, we propose an FPGA-based quality filter to accelerate the filtering step. With the introduction of the One-Hot-encoded accumulator and related modules, the hardware filter can reduce the processing time by half.