Multiple rarefaction?

Is there a way to do multiple rarefactions snd averaging the results when computing the diversity scores?

Hi @akknight216, sorry for the slow response! Have you looked at qiime diversity alpha-rarefaction? That command produces rarefaction curves (similar to in QIIME 1). Alpha diversity metrics are computed a number of times on a range of sampling depths, and that data can be downloaded in CSV format from the visualization. You could load that data into a spreadsheet program or use R/Python/etc. to average the scores. In the rarefaction plots the scores are displayed as medians, so that may also be of use to you.

Note: you’ll want to update to the latest release that just came out (2017.9) because there was an important bug fix in alpha-rarefaction.

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