[khmer] Metagenomics: richness and evenness

[C. Titus Brown]

Eric, thanks, good point!  I was going to respond with "not really" and
leave it at that :).

Upon reflection, I'm not sure partitions will work directly, though.  Things
like 16s, other conserved genes, and repeats break up partitions, so you
tend to get multiple partitions per species.

When we've thought about this, we've mostly discussed finding specific core
genes that are likely to be present in everything, and then separating by DNA
sequence.  The Xander tool might be one way to sensitively extract the core
genes; Jordan, care to comment?

cheers,
--titus

On Thu, May 30, 2013 at 09:23:50AM -0400, Eric McDonald wrote:
> 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,
>   Eric
> 
> 
> 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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> > khmer at lists.idyll.org
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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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-- 
C. Titus Brown, ctb at msu.edu