[khmer] Metagenomics: richness and evenness

Eric McDonald emcd.msu at gmail.com
Thu May 30 06:23:50 PDT 2013

HI Carlos,

I think the partitioning tools in the 'khmer' suite are hypothetically
supposed to produce partitions which match individual species. You could
count the partitions to get an estimate of the richness.

Hope this helps,

On Wed, May 29, 2013 at 7:48 PM, Carlos eduardo <fmafjr at gmail.com> wrote:

> Hello Guys,
> Do you know a way to calculate the richness (number of species) and
>  evenness (abundance of each specie) from a metagenomics sample using k-
> mer (khmer)?
> I saw that khmer can calculate the kmer distribution; however, I don'tknow  if there is an
> approach to calculate the richness and  evenness.
> Thanks
> _______________________________________________
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Eric McDonald
HPC/Cloud Software Engineer
  for the Institute for Cyber-Enabled Research (iCER)
  and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733
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