<div dir="ltr"><div>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.</div>
<div><br></div><div style>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.</div>
<div style><br></div><div style>Jordan</div><div class="gmail_extra"><br><div class="gmail_quote">
On Thu, May 30, 2013 at 11:41 PM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Eric, thanks, good point! I was going to respond with "not really" and<br>
leave it at that :).<br>
<br>
Upon reflection, I'm not sure partitions will work directly, though. Things<br>
like 16s, other conserved genes, and repeats break up partitions, so you<br>
tend to get multiple partitions per species.<br>
<br>
When we've thought about this, we've mostly discussed finding specific core<br>
genes that are likely to be present in everything, and then separating by DNA<br>
sequence. The Xander tool might be one way to sensitively extract the core<br>
genes; Jordan, care to comment?<br>
<br>
cheers,<br>
--titus<br>
<div><br>
On Thu, May 30, 2013 at 09:23:50AM -0400, Eric McDonald wrote:<br>
> HI Carlos,<br>
><br>
> I think the partitioning tools in the 'khmer' suite are hypothetically<br>
> supposed to produce partitions which match individual species. You could<br>
> count the partitions to get an estimate of the richness.<br>
><br>
> Hope this helps,<br>
> Eric<br>
><br>
><br>
> On Wed, May 29, 2013 at 7:48 PM, Carlos eduardo <<a href="mailto:fmafjr@gmail.com" target="_blank">fmafjr@gmail.com</a>> wrote:<br>
><br>
> > Hello Guys,<br>
> ><br>
> > Do you know a way to calculate the richness (number of species) and<br>
> > evenness (abundance of each specie) from a metagenomics sample using k-<br>
> > mer (khmer)?<br>
> ><br>
</div>> > I saw that khmer can calculate the kmer distribution; however, I don'tknow if there is an<br>
<div>> > approach to calculate the richness and evenness.<br>
> ><br>
> > Thanks<br>
> ><br>
> > _______________________________________________<br>
> > khmer mailing list<br>
> > <a href="mailto:khmer@lists.idyll.org" target="_blank">khmer@lists.idyll.org</a><br>
> > <a href="http://lists.idyll.org/listinfo/khmer" target="_blank">http://lists.idyll.org/listinfo/khmer</a><br>
> ><br>
> ><br>
><br>
><br>
> --<br>
> Eric McDonald<br>
> HPC/Cloud Software Engineer<br>
> for the Institute for Cyber-Enabled Research (iCER)<br>
> and the Laboratory for Genomics, Evolution, and Development (GED)<br>
> Michigan State University<br>
> P: <a href="tel:517-355-8733" value="+15173558733" target="_blank">517-355-8733</a><br>
<br>
> _______________________________________________<br>
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<br>
<br>
--<br>
</div>C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
<div><div><br>
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