FAQ: Can I perform single-read runs and still obtain both index sequences? 

Yes. Please select the appropriate workflow based on the flow cell type (single-read or paired- end) when starting your run so that the correct chemistry is used. If using a single-read flow cell, the TruSeq Dual Index Sequencing Primer Box, Single Read (single use box) (Illumina catalog# FC-121-1003) is necessary in order to sequence both index reads.*


* Adapted from Illumina website.