Thank you for sharing this question with us!
I don't know of a pipeline that does this, so instead I'll brainstorm a way to do this from within Qiime2.
Yes. Importantly, 16S amplicons use PCR amplification to target the same part of the game gene which is the same length. This means our tools usually do global alignments so our input sequences need to have end-to-end coverage.
But you have variable lengths:
So let's start here. See if you can extract just one region from all your MAGs, say the 16S V4 region, so you get a list of 16S v4 sequences. This will be like computational PCR, and you can process the results like the 16S v4 sequences from any other study.
Rescript can do this a few different ways. Try this!
Instead of going towards shorter sequences from one variable region, like 16S v4, you could also go towards full length, like you mentioned!
retain near full-length fragments (>1400 bp, or best 1500 bp)
I don't know anything about full length 16S taxonomy, but there has got to be a way!