Assembling Omnitigs using Hidden-Order de Bruijn Graphs

TL;DR

This paper introduces a space-efficient method for navigating variable-order de Bruijn graphs to extract safe strings, improving DNA assembly by capturing more informative sequences than traditional unitigs.

Contribution

It replaces the LCP array with a succinct Cartesian tree representation, enabling efficient navigation and extraction of safe strings in variable-order de Bruijn graphs.

Findings

Extracted more informative strings than unitigs

Used only 2 extra bits per edge for navigation

Achieved efficient safe string extraction in experiments

Abstract

De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well for assembling all of the reads. For this reason, some de Bruijn-based assemblers try assembling on several graphs of increasing order, in turn. Boucher et al. (2015) went further and gave a representation making it possible to navigate in the graph and change order on the fly, up to a maximum $K$, but they can use up to $\lg K$ extra bits per edge because they use an LCP array. In this paper, we replace the LCP array by a succinct representation of that array's Cartesian tree, which takes only 2 extra bits per edge and still lets us support interesting navigation operations efficiently. These operations are not enough to let us easily extract unitigs and only unitigs from the graph but they do let us extract a set of safe strings that contains all unitigs. Suppose we are navigating in a variable-order de Bruijn graph representation, following these rules: if there are no outgoing edges then we reduce the order, hoping one appears; if there is exactly one outgoing edge then we take it (increasing the current order, up to $K$); if there are two or more outgoing edges then we stop. Then we traverse a (variable-order) path such that we cross edges only when we have no choice or, equivalently, we generate a string appending characters only when we have no choice. It follows that the strings we extract are safe. Our experiments show we extract a set of strings more informative than the unitigs, while using a reasonable amount of memory.