<div dir="ltr">HI Carlos,<div><br></div><div style>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.</div>
<div style><br></div><div style>Hope this helps,</div><div style> Eric</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, May 29, 2013 at 7:48 PM, Carlos eduardo <span dir="ltr"><<a href="mailto:fmafjr@gmail.com" target="_blank">fmafjr@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Guys,<div><br></div><div>Do you know a way to calculate the richness (number of species) and evenness (abundance of each specie) from a <span>metagenomics</span> sample using k-<span>mer</span> (<span>khmer</span>)?</div>
<div><br></div><div>I saw that <span>khmer</span> can calculate the <span>kmer</span> distribution; however, I <span>don't</span> know if there is an <span>approach</span> to calculate the richness and evenness.</div>
<div><br></div><div>Thanks</div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Eric McDonald</div><div>HPC/Cloud Software Engineer</div><div> for the Institute for Cyber-Enabled Research (iCER)</div><div> and the Laboratory for Genomics, Evolution, and Development (GED)</div>
<div>Michigan State University</div><div>P: 517-355-8733</div></div>
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