I am using the qiime2-2020.8 conda version and I have used the “qiime feature-table rarefy” plug-in to rarefy an ASV table:
qiime feature-table rarefy --i-table table3.qza --p-sampling-depth 5000 --o-rarefied-table table3-raref.qza
In the qiime2 docs I have read the following information about the rarefy plug-in (rarefy: Rarefy table — QIIME 2 2021.2.0 documentation):
--p-with-replacement / --p-no-with-replacement
Rarefy with replacement by sampling from the
multinomial distribution instead of rarefying without
replacement. [default: False]
I was wondering what is the meaning of default: False. Does it mean that rarefaction is conducted with replacement by default?
I would like to confirm this idea since my rarefied table has a minimum depth of 5,000 reads but not every sample has the same depth (as expected using rarefaction without replacement, I assume).