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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

Alpha diversity metrics

See also
 
Alpha diversity
 
alpha_div command
  alpha_div_rare command
  beta_div command
  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
Name Units Description
richness OTUs Number of OTUs with at least one read for the sample.
 
mirror OTUs See mirror estimator.
 
FE OTUs See singleton-free estimator.
 
chao1 OTUs Chao-1 estimator, calculated as N + S2 / (2 D) where N is the number of OTUs, S is the number of singleton OTUs and D is the number of doublet OTUs, i.e. OTUs with abundance 2.
 
shannon_2 bits Shannon index (logs to base 2).
 
shannon_e nats Shannon index (logs to base e).
 
shannon_10 dits Shannon index (logs to base 10).
 
jost OTUs Jost index of order q where q is specified by the -jostq command-line option, default 1.5.
 
jost1 OTUs Jost index of order 1, the effective number of species given by the Shannon index.
 

Evenness metrics
Name Units Description
simpson Probability 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.
 
dominance
 
Probability Probability that two randomly selected reads will belong to different OTUs. Calculated as 1 - simpson.
 
equitability ? 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 Frequency 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 Frequency 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.
 

 Other
Name Units Description
reads Reads Total number of reads for the sample.