When clustering TruSight Rapid Capture libraries on the cBot and sequencing on the HiSeq 1000/2000, GAIIx, or in High Output mode on the HiSeq 1500/2500, new primers are required whether performing a non-indexed, single-indexed, or dual-indexed run. Use the TruSeq Dual Index Sequencing Primer Box for Paired End runs (catalog # PE-121-1003), which is good for a single run and contains the required primers for sequencing (HP10, HP11, HP12).
For more information, see the Illumina Version Compatibility Reference.