Accelerating De Bruijn Graph-Based Genome Assembly for High-Throughput Short Read Data

Abstract

Emerging next-generation sequencing technologies have opened up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, the generated reads are significantly shorter compared to the traditional Sanger shotgun sequencing method. This poses challenges for de novo assembly algorithms in terms of both accuracy and efficiency. And due to the continuing explosive growth of short read databases, there is a high demand to accelerate the often repeated long-runtime assembly task. In this paper, we present a scalable parallel algorithm to accelerate the de Bruijn graph-based genome assembly for high-throughput short read data.