Parallelizing Big De Bruijn Graph Traversal for Genome Assembly on GPU Clusters

Abstract

De Bruijn graph traversal is a critical step in de novo assemblers. It uses the graph structure to analyze genome sequences and is both memory space intensive and time consuming. To improve the efficiency, we develop ParaGraph, which parallelizes De Bruijn graph traversal on a cluster of GPU-equipped computer nodes. With effective vertex partitioning and fine-grained parallel algorithms, ParaGraph utilizes all cores of each CPU and GPU, all CPUs and GPUs in a computer node, and all computer nodes of a cluster. Our results show that ParaGraph is able to traverse billion-node graphs within three minutes on a cluster of six GPU-equipped computer nodes. It is an order of magnitude faster than the state-of-the-art shared memory based assemblers, and more than five times faster than the current distributed assemblers.