Question: Is the Sample Index PCR required if not multiplexing samples?
Answer: The Sample Index PCR is required even if only one sample will be sequenced (i.e. not multiplexed for sequencing). During the Sample Index PCR, not only are the sample indexes added, but P5 and P7 adapters are also added. The P5 and P7 sequences are critical for hybridization to the Illumina flow cell and sequencing.