OTU / denoising pipeline
Which taxonomy database should I use?
Interpreting diversity metrics
Recommended alpha and beta metrics
Comparing alpha diversity between groups
Statistical significance of diversity differences
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.
You can visualize diversity using octave plots.
Note that most standard diversity metrics are difficult to interpret or invalid for NGS OTUs.
You can test for
differences in alpha diversity between groups by using the
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_aggd command.