So, I am new to the whole bioinformatics game and I am in the process of learning. I was curious if I could use Trimmomatic software for trimming barcodes, adaptors, and primers off my sequences and then enter it into qiime2 for further processing and taxonomy assignment. I would like to use Dada2 and Deblur to test the results. Any helpful information would be awesome.
I would recommend using q2-cutadapt to trim off adapters/primers instead of trimmomatic:
The advantage is that this is all in QIIME 2, so the steps get stored in the provenance tracking, and you are much less likely to run into formatting issues.
In theory, using trimmomatic should be fine, but we have had some users report issues after attempting to import those data into QIIME 2. So go for it, but search the archive on this forum for "trimmomatic" to see other formatting troubleshooting that others have needed to do in the past.
Good luck!