Edge minimization in de Bruijn graphs

Edge minimization in de Bruijn graphs

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)

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Authors
  • Baier, Uwe
  • Büchler, Thomas
  • Ohlebusch, Enno
  • Weber, Pascal
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Shortfacts
Category
Journal Paper
Divisions
Data Mining and Machine Learning
Journal or Publication Title
CoRR arXiv
ISSN
arXiv:1911.00044
Date
31 October 2019
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