Hey @Coke_Lin,
We definitely don’t have anything that handles PacBio data yet. We don’t really have much collective experience with it either. That being said, QIIME 2 is super extensible so if you knew some developers who interested in adding the formats and any QC needed, it should be pretty straight-forward (and we’d be happy to answer questions along the way).
Also depending on what the data is (e.g. amplicon vs shotgun vs long single molecule) there may not necessarily be the “downstream” analysis available yet either. We’ve focused mostly on amplicon data so far (and will continue to up to 2018.1), but someday we’ll have support for other kinds.