In the R DADA2's library the actual algorithm to infer the ASVs can run with three different pooling methodologies, i.e. independent, pseudo, and what I call full-pooling, i.e. the one where
pool=TRUE, as shown here.
# independent system.time(dd <- dada(drp, err=err, multithread=TRUE, pool=FALSE, verbose=0))
# pseudo system.time(dd.pseudo <- dada(drp, err=err, multithread=TRUE, pool="pseudo", verbose=0))
# full-pooling system.time(dd.pool <- dada(drp, err=err, multithread=TRUE, pool=TRUE, verbose=0))
On the other hand, in the manual page for
denoise-paired of the Qiime2's DADA2 plugin, there is no mention concerning the full-pooling:
--p-pooling-method TEXT Choices('independent', 'pseudo')
The method used to pool samples for denoising.
"independent": Samples are denoised indpendently.
"pseudo": The pseudo-pooling method is used to
approximate pooling of samples. In short, samples are
denoised independently once, ASVs detected in at
least 2 samples are recorded, and samples are
denoised independently a second time, but this time
with prior knowledge of the recorded ASVs and thus
higher sensitivity to those ASVs.
My question is: clearly we can't run the full pooling as we can with the R version of the package, right? Am I missing something, here?