eliminating single sample with low number of sequences

I am curious if there is code available to eliminate a single sample from my analysis. I reached the part of the SOP where it is recommended to subsample to the lowest number of sequences. However, I found a sample with only 44 sequences. As this number is really low and after going through my lab notes this sample likely did not have enough DNA extracted, I would like to ignore this sample and subsample to the sample with the next lowest number of sequences (31,482)

I think the remove.groups command would be helpful for you, http://www.mothur.org/wiki/Remove.groups.