FAQ: Do I need to spike in custom sequencing primers when sequencing libraries are made with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2) on Illumina sequencing instruments?

No. Libraries made using NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 2) are fully compatible with Illumina sequencing protocols for TruSeq® HT libraries. For HiSeq®, HiScan®SQ, or GAIIx® systems on single-read flow cells, the TruSeq Dual Index Sequencing Primer Box, Single Read (single use box) (Illumina catalog # FC-121-1003) will need to be ordered separately when using both indices. This add-on box is not required with the MiSeq® System or on paired-end flow cells for HiSeq, HiScanSQ, GAIIx. Please refer to the Illumina website for complete information.