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Old 11-15-2015, 05:23 AM   #1
TauOvermind
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Default 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:

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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.
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Old 11-16-2015, 09:20 AM   #2
Brian Bushnell
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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.
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Old 11-17-2015, 10:28 AM   #3
TauOvermind
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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 at 10:55 AM.
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