TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes.

Abstract

de Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes). In this article, we present TwoPaCo, a simple and scalable low memory algorithm for the direct construction of the compacted de Bruijn graph from a set of complete genomes. We demonstrate that it can construct the graph for 100 simulated human genomes in less than a day and eight real primates in < 2 h, on a typical shared-memory machine. We believe that this progress will enable novel biological analyses of hundreds of mammalian-sized genomes. Our code and data is available for download from github.com/medvedevgroup/TwoPaCo. ium125@psu.edu. Supplementary data are available at Bioinformatics online.