Coverage estimation by autosimilarity

Feature requests
1

Hi,
have you heard of calculating the ‘autosimilarity’ of a sample to estimate the coverage, as an alternative to Good’s coverage? (Cao et al, 2002, Ecol. Monogr.)
Is it already a feature in Mothur? I couldn’t find it. And do you know if it’s “better” than Good’s coverage?

In relation to this, I’ve read something about standarizing rarefaction and other estimators by an estimate of the coverage of the sample rather than sample size? Has anyone used this?

Many thanks and good luck.

Fred

2

Hi,

I have been interested in rarefaction based standardization. Do you have a reference for that, that I can look up?

Thanks,
Ameet

3

Hi Ameet,
there is a chapter in Methods in Enzimology - Env. Microbiology.
“The Application of Rarefaction Techniques to Molecular Inventories of Microbial Diversity”, by Hughes&Hellmann.
Maybe you find something interesting there.