DeepAI AI Chat
Log In Sign Up

Edge minimization in de Bruijn graphs

by   Uwe Baier, et al.

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. This also gives an affirmative answer to the open problem of finding optimal disjoint blocks that minimize space, as stated in Alanko et al. (DCC 2019).


page 1

page 2

page 3

page 4


Efficient constructions of the Prefer-same and Prefer-opposite de Bruijn sequences

The greedy Prefer-same de Bruijn sequence construction was first present...

The Open Problem of Finding a General Classification of Geodetic Graphs

This note describes some open problems that can be examined with the pur...

An Efficient Algorithm for All-Pairs Bounded Edge Connectivity

Our work concerns algorithms for an unweighted variant of Maximum Flow. ...

Finding Diverse Minimum s-t Cuts

Recently, many studies have been devoted to finding diverse solutions in...

On the Hardness and Inapproximability of Recognizing Wheeler Graphs

In recent years several compressed indexes based on variants of the Borr...

Infinite Lewis Weights in Spectral Graph Theory

We study the spectral implications of re-weighting a graph by the ℓ_∞-Le...

Optimal Network Compression

This paper introduces a formulation of the optimal network compression p...