From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

  • Nikolay Vyahhi
  • Alex Pyshkin
  • Son Pham
  • Pavel A. Pevzner
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)


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 .


Jigsaw Puzzle Fragment Assembly Puzzle Problem Eulerian Cycle Matching Side 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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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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