Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly

  • Son K. Pham
  • Dmitry Antipov
  • Alexander Sirotkin
  • Glenn Tesler
  • Pavel A. Pevzner
  • Max A. Alekseyev
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)

Abstract

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Son K. Pham
    • 1
  • Dmitry Antipov
    • 1
  • Alexander Sirotkin
    • 2
  • Glenn Tesler
    • 3
  • Pavel A. Pevzner
    • 1
    • 2
  • Max A. Alekseyev
    • 2
    • 4
  1. 1.Dept. of Computer Science and EngineeringUniversity of CaliforniaSan DiegoUSA
  2. 2.Algorithmic Biology LaboratorySt. Petersburg Academic UniversitySt. PetersburgRussia
  3. 3.Dept. of MathematicsUniversity of CaliforniaSan DiegoUSA
  4. 4.Dept. of Computer Science and EngineeringUniversity of South CarolinaColumbiaUSA

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