Alpha diversity metrics
Interpreting diversity metrics
Recommended alpha and beta metrics
Comparing alpha diversity between groups
Statistical significance of diversity differences
While many of these alpha diversity metrics are commonly used in OTU analysis, in fact many of them are invalid or hard to interpret for OTUs constructed from NGS amplicon reads.Diversity metrics
||Simpson index, calculated as the sum over OTUs of f2 where f is the frequency of the OTU. It is the probability that two randomly selected reads will belong to the same OTU. A value close to 1 indicates that a single large OTU dominates the sample, small values indicate that the reads are distributed over many OTUs.
||Probability that two randomly selected reads will belong to different OTUs. Calculated as 1 - simpson.
||Also called Peilou's evenness. Entropy (Shannon index) divided by the logarithm of the number of OTUs. Value of 1 indicates perfectly even (equal abundances), small values indicate a highly skewed abundance distribution.
||Robbins index, calculated as S / (N + 1) where S is the number of singleton OTUs and N is the total number of OTUs.
||Berger-Parker index. Frequency of the most abundant OTU. A value close to 1 indicates that a single large OTU dominates the sample, small values indicate that the reads are distributed over many OTUs.
||Total number of reads for the sample.