Question: VelvetOptimizer always chooses 31 as the kmer length and never looks further than that?
0
gravatar for katherine.lavoie
2.5 years ago by
katherine.lavoie0 wrote:

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!

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by katherine.lavoie0
2

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 2.5 years ago • written 2.5 years ago by genomax71k
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