Comparative genomics with succinct colored de Bruijn graphs

TL;DR

This paper introduces gcBB and mgcBB, novel methods for direct genome comparison using succinct colored de Bruijn graphs, avoiding sequence alignments and leveraging entropy measures for improved phylogenetic analysis.

Contribution

The paper presents gcBB and mgcBB, innovative tools for genome comparison based on succinct colored de Bruijn graphs, enhancing efficiency and accuracy over existing methods.

Findings

gcBB effectively compares draft genomes without alignments.

mgcBB significantly improves computational performance.

Phylogenies derived from gcBB show promising accuracy.

Abstract

DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations complicate obtaining the complete sequence of 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 draft genomes by comparing paths in de Bruijn graphs, which are constructed by many practical genome assemblers. In this article we introduce gcBB, a method for comparing genomes represented as succinct colored de Bruijn graphs directly, without resorting to sequence alignments, by means of the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution. We also introduce an improved version of gcBB, called mgcBB, that improves the time performance considerably through the selection of different data structures. We have compared phylogenies of genomes obtained by other methods to those obtained with gcBB, achieving promising results.