What is the best way to calculate the biological diversity of samples from bacterial/viral OTU tables?
I have a few large OTU tables of bacterial and viral datasets. The samples are across different sites and times.
I would like to visualise the community 'diversity' across the times for which I have data. For example it would be interesting to see if community diversity peaks in the summer months and falls in the winter months- in a repeating pattern.
I have not come across much advice or literature which looks at looking at diversity for large OTU datasets. Considering the OTUs are essentially arbitrary and that there are thousands of them, what is the best way to calculate and visualise the each samples diversity?
With the vegan package on R it is quite easy to calculate the Shannon/Simpsons diversity index for an OTU table. Can you simply use this on a 'raw' table of OTUs?
Most people are using rarefaction (curves) to assess species richness and diversity based on OTU count tables. I would recommend following the SOP for QIIME 2.
