Nextera XT adapter trimming


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!

Hi there,

You will want to use make.contigs using the oligos option where you insert into an oligos file your barcodes and primers. I don’t think the seqeunces should have the adapters themselves, but I think they should probably start with the barcodes and then the primers. Can you run on one of the files and then post the first 10 sequences along with what you think the adapters, barcodes, and primers are?