An FPGA-based quality filter for de novo sequence assembly pipeline

Abstract

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.