Question: VelvetOptimizer always chooses 31 as the kmer length and never looks further than that?
gravatar for katherine.lavoie
2.1 years ago by
katherine.lavoie0 wrote:


I run this line: -d 'outputfolder' -s 21 -e 91 -f '-fasta -shortPaired ./myfile.fasta'

and velvetoptimizer always gives me a result of 31 as my ideal Kmer. it doesnt even test beyond that.

I dont really understand what I am doing wrong can anyone help me or explain my VelvetOptimizer always goes to its default parameter for kmer length to test?

Thank you!

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by katherine.lavoie0

By default velvet uses a maxkerlength of 31 which is what you are seeing. You need to re-compile velvet if you want to use longer kmers. Do you have a reason to believe velvet could benefit from using longer k-mers?

I will link these threads on how to make the necessary change: Velvet can't handle k-mers as long as X! We'll stick to 32 if you don't mind. and Question: Can't change MAXKMERLENGTH on Velvet

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax63k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1785 users visited in the last hour