Motivation: 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). Results: 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.
TwoPaCo REF uses a bloom filter to represent the ordinary de Bruijn graph and then constructs the compacted de Bruijn graph from the bloom filter encoded one.
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
Bioinformatics
Computer Science Mathematics Biology Medicine