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Taxonomy and diversity analysis

See also
  OTU / denoising pipeline
  Alpha diversity
  Beta diversity
  Rarefaction
  Which taxonomy database should I use?

Diversity analysis investigates questions such as "how many species are in a sample?" and "how similar are these two samples?". The diversity in a single sample is called alpha diversity, and the diversity (differences or similarities) between two samples is called beta diversity.

The input data used for diversity analysis is an OTU table. A tree for the OTUs is also needed for UniFrac beta diversity analysis, this can be created using the cluster_agg command.

Usearch supports diversity analysis through the alpha_div, alpha_div_rare and beta_div commands. These commands support several popular diversity metrics.

Note that most standard diversity metrics are difficult to interpret or invalid for NGS OTUs.
 
Taxonomy for the OTU sequences can be predicted using the sintax command
. See also Which taxonomy database should I use?
 
A tree for the OTU sequences can be generated using the cluster_agg command
.