A de novo genome assembler based on MapReduce and bi-directed de Bruijn graph

The next generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. Assembly of NGS reads still face great challenges due to the short reads and enormous high volume. In this paper, we presented a new assembler, called GAMR, which is based on bi-directed de Bruijn graph and implemented using MapReduce framework. We designed distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We evaluated GAMR using GAGE's data and compared it against other NGS assemblers. The results showed GAMR assembled contigs and scaffolds with better accuracy and longer N50 values.