Question: VelvetK long Kmers
gravatar for samuel.lipworth
2.5 years ago by
University of Oxford
samuel.lipworth30 wrote:

I have been using velvetK to estimate optimal Kmer lengths and then plugging these into velvet optimiser. When I then annotate these assemblies (using Prokka) and stick them through Roary, they seem to group by assembly length rather than true phylogeny. I know the reads are not nonsense because when I assemble them using a reference genome the phylogeny makes sense so I think the problem is my denovo assembly. Any ideas as to how I could improve this?

ADD COMMENTlink written 2.5 years ago by samuel.lipworth30

It would be helpful to describe what you are trying to assemble; the sequencing platform; library prep; run mode / read length; preprocessing you have attempted; etc.

ADD REPLYlink written 2.5 years ago by Brian Bushnell16k
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: 1677 users visited in the last hour