Sequencing libraries prepared with the Illumina Nextera DNA Sample Preparation Kit on the HiSeq 2000, HiSeq 1000, or HiScanSQ, requires the TruSeq Dual Index Sequencing Primer Box for cluster generation and sequencing.
See Nextera DNA Sample Preparation Kit Compatibility for HiSeq 2000, HiSeq 1000, or HiScanSQ .
Sequencing libraries prepared with the Illumina Nextera DNA Sample Preparation Kit on the MiSeq does not require any additional sequencing primers. The primers are included in the MiSeq Reagent Kit.
See Nextera DNA Sample Preparation Kit Compatibility for MiSeq.