OTU / denoising pipeline
The fastx_uniques command can be to find the unique sequences and add the size annotations.
Finding unique sequences is sometimes called "dereplication".
I suggest you use -relabel Uniq so that the unique sequences are labeled Uniq1, Uniq2 and so on. The input to fastx_uniques should be the reads after any quality filtering or length trimming.
Samples should be pooled before dereplication
I recommend pooling samples, i.e. concatenating reads for all samples that were sequenced in the same run. This is important for getting the best detection of chimeras and cross-talk, and for getting the best sensitivity to low-abundance sequences that could be lost if individual samples or subsets of samples are clustered separately. See pooling samples for discussion.