Hi @Sara_Jeanne08 - I kinda figured you had DI data, but thought "just in case...".
Are you talking about joining forward and reverse reads, or, joining your barcodes back into your reads?
I am about to start working on supporting DI demultiplexing with q2-cutadapt (open issue here), where the barcodes are in the reads (as opposed to the fastq header, or a separate file, like your case). We also have an outstanding ticket that @colinbrislawn linked to above to support DI demultiplexing for EMP protocol data, which is basically what you have. It is safe to say that the q2-cutadapt solution will be in place first, so if you have a way to "re-attach" your barcodes to your reads, you could use this new method when it is released (maybe 2017.2?).
As far as read joining goes (well, joining forward and reverse reads), this is accomplished in QIIME 2 in a few ways. First, the denoise methods in q2-dada2 join PE reads (this is how DADA2 works generally speaking, outside of Q2). Please note, DADA2 actually relies on processing unjoined PE data - the error model won't work as expected if you provide already joined reads, so please keep that in mind! We also have a q2-vsearch method for joining reads, which is helpful if you are going to use deblur, or one of the OTU-based methods in q2-vsearch.
RE chimeras, I don't know if it makes more sense for you to remove pre-import or not, but, in case you haven't seen it, we have a community tutorial for removing chimeras using q2-vsearch.
Stay tuned, and thanks for writing! 