I am writing this thread with regards to nextera XT adapter trimming in mothur.
In my previous Miseq library preps for ITS sequencing, I have used barcodes with the forward are reverse primers as identifiers for each sample. After running the make.contig command I used to use an Oligos file with the primer and barcode sequencing for trimming and that worked as expected.
We have currently moved to library prep at a sequencing facility where they use Nextera XT sets A, B, C, and D. I am unsure how to proceed with trimming the Nextera adapters. Can anyone provide insight on how to proceed?
Thank you in advance!