pcr.seqs can be skipped for clean reads?

Hi, is it correct that if my NGS reads do not contain primers, linkers, barcodes, etc, ie they are “clean” sequences, there is no need to run pcr.seqs to trim them?
Thanks a lot.

You wouldn’t want to use pcr.seqs to trim them anyway… As laid out in the MiSeq SOP the sequences we use do not contain any of the primers, linker, or barcodes. I would suggest starting there.