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
Paper in Conference Proceedings or in Workshop Proceedings (Paper)
Event Title
30th Data Compression Conference (DCC)
Divisions
Data Mining and Machine Learning
Event Location
Snowbird, UT, USA
Event Type
Conference
Event Dates
24-27.03.2020
Series Name
Data Compression Conference (DCC)
ISSN/ISBN
978-1-7281-6457-1
Date
24 March 2020
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