Gap Filling as Exact Path Length Problem

  • Leena SalmelaEmail author
  • Kristoffer Sahlin
  • Veli Mäkinen
  • Alexandru I. Tomescu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)


One of the last steps in a genome assembly project is filling the gaps between consecutive contigs in the scaffolds. This problem can be naturally stated as finding an \(s\)-\(t\) path in a directed graph whose sum of arc costs belongs to a given range (the estimate on the gap length). Here \(s\) and \(t\) are any two contigs flanking a gap. This problem is known to be NP-hard in general. Here we derive a simpler dynamic programming solution than already known, pseudo-polynomial in the maximum value of the input range. We implemented various practical optimizations to it, and compared our exact gap filling solution experimentally to popular gap filling tools. Summing over all the bacterial assemblies considered in our experiments, we can in total fill 28% more gaps than the best previous tool and the gaps filled by our method span 80% more sequence. Furthermore, the error level of the newly introduced sequence is comparable to that of the previous tools.


Source Vertex Multidimensional Knapsack Problem Assembly Graph Dynamic Programing Table Previous Tool 
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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Leena Salmela
    • 1
    Email author
  • Kristoffer Sahlin
    • 2
  • Veli Mäkinen
    • 1
  • Alexandru I. Tomescu
    • 1
  1. 1.Helsinki Institute for Information Technology HIIT, Department of Computer ScienceUniversity of HelsinkiHelsinkiFinland
  2. 2.Science for Life Laboratory, School of Computer Science and CommunicationKTH Royal Institute of TechnologySolnaSweden

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