Abundance rarefaction

**See also**

Rarefaction

alpha_div_rare command

Suppose you observe *K* different species, finding
*N _{k}* individuals in the

My colleague Henrik Flyvbjerg and I have developed the modified formula for*
S*(*n*)* *when singletons are discarded; let me know if
you are interested and I will send you the details.

**Rarefaction for OTUs
**If species with exactly one observation are ignored, then the
above formula does not apply. Thus, if singleton
reads are discarded, as recommended in the
UPARSE pipeline, then you cannot use standard rarefaction software and the
above formula does not give the correct result. If singletons are retained, then
the formula is a reasonable approximation, but is not exactly correct because

With *de novo *OTUs, including those made by
UPARSE, then strictly speaking,
rarefaction curves must be generated by running the pipeline from scratch for
each random subsample and noting the number of OTUs obtained.