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  • What is the effect of modulating the gaplenDiff parameter -G in SOAPdenovo2?

    Hello Seqanswers! Long time reader, first time questioner.

    I'm trying to figure out what the effect of changing the gaplenDiff parameter is, as the documentation doesn't thoroughly address it (neither paper nor the supp), and there's no google-able explanation to what the parameter does. I'm still a neophyte when it comes to de novo genome assembly, and the authors' explanation at the SOAP page "-G <int> gapLenDiff: allowed length difference between estimated and filled gap, [50]" isn't sufficient for me to build an intuitive understanding of what the parameter is, as I don't understand the intended distinction of estimated gap versus filled gap.

    Thanks very much for any insights- cheers!

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