[khmer] less reads but more kmers?

[Nacho Caballero]

I used khmer to digitally normalize two assemblies:

   - After normalization, Assembly A has *1.5 million reads*, and during
   assembly SPAdes uses *116 million* kmers (k=37)
   - After normalization, Assembly B has *1.5 million reads*, during
   assembly SPAdes uses *612 million* kmers (k=37)

I followed the same protocol on both assemblies (quality filtering with
Trimmomatic, 3-pass normalization, etc.), so I don’t understand why
assembly B, with 16x fewer reads, has 8x more kmers than assembly A.

What are some possible explanations?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20140117/5f179289/attachment-0001.htm>