VelvetOptimizer always chooses 31 as the kmer length and never looks further than that?

Question

[katherine.lavoie]

Hello!

I run this line:

VelvetOptimiser.pl -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!

[GenoMax]

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