[khmer] Metagenomics: richness and evenness

[Jordan Fish]

Using targeted assembly (Xander) for core gene extraction should be pretty
straight forward although as of right now the only core gene I've tested is
rplb. I think this approach should be able to give you a decent estimate of
richness.

The only two complications I can see are identifying a set of core genes,
and then trying to combine all the core gene assembly information together
(and, more importantly, missing information) to get a final richness count.

Jordan

On Thu, May 30, 2013 at 11:41 PM, C. Titus Brown <ctb at msu.edu> wrote:

> 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
> > > http://lists.idyll.org/listinfo/khmer
> > >
> > >
> >
> >
> > --
> > 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
>
> > _______________________________________________
> > khmer mailing list
> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer
>
>
> --
> C. Titus Brown, ctb at msu.edu
>
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