From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

  • Nikolay Vyahhi
  • Alex Pyshkin
  • Son Pham
  • Pavel A. Pevzner
Conference paper

DOI: 10.1007/978-3-642-33122-0_20

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)
Cite this paper as:
Vyahhi N., Pyshkin A., Pham S., Pevzner P.A. (2012) From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. In: Raphael B., Tang J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science, vol 7534. Springer, Berlin, Heidelberg

Abstract

Jigsaw puzzles were originally constructed by painting a picture on a rectangular piece of wood and further cutting it into smaller pieces with a jigsaw. The Jigsaw Puzzle Problem is to find an arrangement of these pieces that fills up the rectangle in such a way that neighboring pieces have “matching” boundaries with respect to color and texture. While the general Jigsaw Puzzle Problem is NP-complete [6], we discuss its simpler version (called Rectangle Puzzle Problem) and study the rectangle graphs, recently introduced by Bankevich et al., 2012 [3], for assembling such puzzles. We establish the connection between Rectangle Puzzle Problem and the problem of assembling genomes from read-pairs, and further extend the analysis in [3] to real challenges encountered in applications of rectangle graphs in genome assembly. We demonstrate that addressing these challenges results in an assembler SPAdes+ that improves on existing assembly algorithms in the case of bacterial genomes (including particularly difficult case of genome assemblies from single cells).

SPAdes+ is freely available from http://bioinf.spbau.ru/spades.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Nikolay Vyahhi
    • 1
  • Alex Pyshkin
    • 1
  • Son Pham
    • 2
  • Pavel A. Pevzner
    • 1
    • 2
  1. 1.Algorithmic Biology LaboratorySt. Petersburg Academic UniversityRussia
  2. 2.Department of Computer Science and EngineeringUCSDLa JollaUSA

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