Fasta_diversity command in Usearch
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!
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andreavidaldura •
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andreavidaldura •
1 answer
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.
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Istvan Albert
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