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  • TauOvermind
    Member
    • Jul 2012
    • 14

    #1

    Minimal overlap between two reads in the de Bruijn algorithm

    I was reading a paper named "Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph" by Zhenyu Li et al. (2011), when I came across the following sentence:

    In the DBG algorithm, to ensure the k-mers can be linked, the minimum overlap between two reads should be no less than the k-mer size K that is equivalent to the T parameter in the Lander–Waterman model.
    I thought that the minimum overlap between two reads should be no less than K-1 and not K. I would really appreciate it if someone could explain me the quoted statement.
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709

    #2
    Originally posted by TauOvermind View Post
    I thought that the minimum overlap between two reads should be no less than K-1 and not K. I would really appreciate it if someone could explain me the quoted statement.
    Yes, you're right. In practice there's so little difference between K and K-1 that it's easy to make a mistake like that and overlook it.

    Comment

    • TauOvermind
      Member
      • Jul 2012
      • 14

      #3
      Thank you, Brian. I agree that the difference between these two values would be minimal in practice, but as it was a paper about the theory of sequence assembly, I found that statement confusing, as I thought that I might have been missing an important point in the derivation.
      Last edited by TauOvermind; 11-17-2015, 11:55 AM.

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