Custom sequencing primers can enable some unique assays. However, it is certainly worth exploring if the assays can not be converted to use standard Illumina sequencing primers.
Custom sequencing primers can be used for all reads on the Miseq and NextSeq sequencers. Illumina does not support custom primers on the HiSeq 4000 at all, but we can spike them in for the forward read.
Please provide an aliquot for each custom primer (10 ul at 100 uM) with the library submission. Please note that the customer carries the responsibility for any failures due to bad custom primers or poorly designed custom primers.