ABySS genome assembler

Question

[npavliukovec]

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?

[GenoMax]

Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc

[npavliukovec]

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

Answer 1

[shelkmike]

You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.