Edge minimization in de Bruijn graphs

TL;DR

This paper presents an efficient algorithm for minimizing edges in de Bruijn graphs, which improves graph compression and enhances sequence analysis by optimizing BWT tunneling techniques.

Contribution

It introduces a novel algorithm for edge minimization in de Bruijn graphs and connects this to BWT tunneling, advancing solutions for graph compression and sequence analysis.

Findings

Efficient algorithm for edge minimization in de Bruijn graphs

Improved BWT tunneling with preserved properties for analysis

Progress towards optimal disjoint block solutions in graph compression

Abstract

This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that solves this problem. Since the edge minimization problem is connected to the BWT compression technique called "tunneling", the paper also describes a way to minimize the length of a tunneled BWT in such a way that useful properties for sequence analysis are preserved. Although being a restriction, this is significant progress towards a solution to the open problem of finding optimal disjoint blocks that minimize space, as stated in Alanko et al. (DCC 2019).