Hello, I have to assembly using ABySS. But I could not get how I should calculate the optimal size of k-mer. So may be anyone know the method or program to calculate it?
Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abyss-fac command, cuz it is not installed. In this way I am trying to find another way to calculate optimal k-mer size
You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
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