I filtered different amount of sea water and we did Illumina sequencing on the samples obtained. To be able to compare among different samples I would standardize the samples by calculating the OTU reads per liter.

I found that Quime suggests standardization to the minimum otbained to reduce noise. But since I dont work with the FASTA format but with an excel table with the reads of OTUs which are assigned to the different species I obtained, I am wondering if calculating OTUs per Liter would be a standarization method which allows me to compare among my 33 different samples?

How do you standardize your HTS data of environmental samples?