Scalable de Novo Genome Assembly Using a Pregel-Like Graph-Parallel System

De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-Throughput genome sequencing and thus accelerates the discovery of new genomes. In this paper, we present a toolkit, called PPA-Assembler, for de novo genome assembly in a distributed setting. The operations in our toolkit provide strong performance guarantees, and can be assembled to implement various sequencing strategies. PPA-Assembler adopts the popular de Bruijn graph based approach for sequencing, and each operation is implemented as a program in Google's Pregel framework which can be easily deployed in a generic cluster. Experiments on large real and simulated datasets demonstrate that PPA-Assembler is much more efficient than the state-of-The-Arts while providing comparable sequencing quality. PPA-Assembler has been open-sourced at https://github.com/yaobaiwei/PPA-Assembler.