reproducing alpha rarefaction with python

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1

Hello everyone !

Is there a way to reproduce the alpha rarefaction curve within python from the csv file included in alpha- rarefaction.qza.

Regards,

Manil

2

Hi @BiOMan,

You’re got a few options. You could run it in QIIME and open the visualisation and then download the csv. I’d read that in via pandas and then make my plot. You could try the python API to generate your rarefaction curve, and then extract to a series or DataFrame, and then generate the curve from that, or you could use a biom Table object to do your rarefaction, calculate alpha diversity via scikit-bio, generate a DataFrame from those values, and then plot.

I think your path of least resistance will be the first.

Best,
Justine

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3

Hi Justine,

Thank you very much for your reply and sorry for my late answer ! Indeed I have opted for the the first solution and it works. The purpose is, I am automizing a pipeline for 16S amplicon sequencing analysis for clinical report for each patient (Crohn’s patients), so that’s why I didn’t use the .qzv for visualization .

Regards,

Manil

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