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?
Question: VelvetK long Kmers
2.2 years ago by
samuel.lipworth • 30
University of Oxford
samuel.lipworth • 30 wrote:
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