FAQ: Can I perform single read runs and still get both index sequences? Can I run both single read and paired-end recipes with dual-indexed libraries?

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) (catalog #FC-121-1003) is necessary in order to sequence both index reads. 

Adapted from Illumina website.