Genome Comparison on Succinct Colored de Bruijn Graphs

The improvements in DNA sequence technologies have increased the volume and speed at which genomic data is acquired. Nevertheless, due to the difficulties for completely assembling a genome, many genomes are left in a draft state, in which each chromosome is represented by a set of sequences with partial information on their relative order. Recently, some approaches have been proposed to compare genomes by comparing extracted paths from de Bruijn graphs and comparing such paths. The idea of using data from de Bruijn graphs is interesting because such graphs are built by many practical genome assemblers. In this article we introduce gcBB, a method for comparing genomes represented as succinct de Bruijn graphs directly, without resorting to sequence alignments, by means of the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution (BWSD). We have compared phylogenies of genomes obtained by other methods to those obtained with gcBB, achieving promising results.