Fasta_diversity command in Usearch

Question

[andreavidaldura]

Hi all,

I am currently doing alpha diversity analysis of individual samples (sequenced by Illumina). I am playing with the Usearch commands and I have some questions about the -fasta_diversity command:

• In the output file what are the two first columns (Pct and N)?
• What means exactly the -iters option suggested in the example: http://drive5.com/usearch/manual/cmd_fasta_diversity.html

I found that it means number of iterations to try for each subset size but I don't really know what it does here.

Thank you everybody!

Answer 1

[Istvan Albert]

rarefaction is computed by resampling randomly, the iter parameter most likely indicates how many resamplings to take

Pct sounds like percent, N sounds like the total number.