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This article is part of the supplement: Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)

Open Access Proceedings

De Bruijn Superwalk with Multiplicities Problem is NP-hard

Evgeny Kapun and Fedor Tsarev*

Author Affiliations

St. Petersburg National Research University of Information Technologies, Mechanics and Optics Genome Assembly Algorithms Laboratory 197101, Kronverksky pr., 49, St. Petersburg, Russia

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BMC Bioinformatics 2013, 14(Suppl 5):S7  doi:10.1186/1471-2105-14-S5-S7

Published: 10 April 2013

Abstract

De Bruijn Superwalk with Multiplicities Problem is the problem of finding a walk in the de Bruijn graph containing several walks as subwalks and passing through each edge the exactly predefined number of times (equal to the multiplicity of this edge). This problem has been stated in the talk by Paul Medvedev and Michael Brudno on the first RECOMB Satellite Conference on Open Problems in Algorithmic Biology in August 2012. In this paper we show that this problem is NP-hard. Combined with results of previous works it means that all known models for genome assembly are NP-hard.