ABySS genome assembler
1
0
Entering edit mode
13 months ago

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?

ABySS genome k-mers assembly • 999 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
13 months ago
shelkmike ★ 1.2k

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

ADD COMMENT

Login before adding your answer.

Traffic: 3932 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6