ABySS genome assembler
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?
• 2,130 views
•
link
updated
by
shelkmike
•
written
by
npavliukovec •
•
written
by
npavliukovec •
1 answer
You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
Log in to answer this question.
More posts like this
-
What could be a better K-mer for my WGS assembly task using ABySS, with my current hardware profile.
written by Vijith •
-
How to choose k-mer for the genome size estimation?
written by 524730309 •
-
abyss-pe crashes when ran on 650k+ reads
written by nsapoval •
-
Running ABySS at k-mer > 97
written by Anand Rao
-
How to find Bloom filter parameter for Abyss 2
written by Ric
-
Denovo Assemly of unmapped reads
written by sukesh1411 •
-
gap size between k-mer pairs
written by balaani •
-
How To Count K-Mer For Color-Space Reads?
written by GAO Yang
-
How To Estimate Genome Size Using K-Mer Coverage
written by GAO Yang
-
Abyss Speed-Up Tricks
written by Darked89
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