It's a trade off, since 63 requires more memory for storage, but allows you to use larger kmer values. For data from newer sequencing technologies, where the individual sequences are longer, this can yield better assembly results, but it varies widely depending on the data. Most people perform a parameter sweep of kmer values.

We definitely want OPENMP and LONGSEQUENCES as defaults, but I'm sure about the kmer size. For all the work I do, I always need 63, or sometimes even 127, but I'm not sure what others would need.

Mark

On Jan 23, 2013, at 4:07 PM, Samuel John <notifications@github.com> wrote:

> In velvet.rb:
> 
> > @@ -7,12 +7,27 @@ class Velvet < Formula
> >  
> >    head 'https://github.com/dzerbino/velvet.git'
> >  
> > +  option 'with-63mer', "Build with maximum kmer length of 63 instead of 31"
> Is 63 better? Shall we default to 63?
> 
> —
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