Question on alpha diveristy

[LanSabb]

Hi @wwood

I have two questions on the computation of the alpha diversity

Question 1. What would be proper input types for alpha diversity estimation ?
(1) num_hits from raw OTU data
(2) coverage values from raw OTU data
(3) num_hits from rarefied OTU data
(4) etc ?

Question 2. Fourteen ribosomal protein marker genes will be used to calculate the alpha diversity. To calculate the alpha diversity, it seems to be necessary to sum up the counts of each markers per species and divide it by number of markers. Does SingleM have a submodule for this procedure? Would you recommend any tool to support this function ?

Thanks !