Scalable De Novo Genome Assembly Using Pregel

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. PPA-assembler adopts the popular de Bruijn graph based approach, and the operations run on Google's Pregel framework with strong performance guarantees. PPA-assembler demonstrates superior performance compared with existing assemblers, and is open-sourced at https://github.com/yaobaiwei/PPAAssembler. The full version of this paper can be found at https://arxiv.org/abs/1801.04453.