FAQ: Can I run both single read and paired-end recipes with dual-indexed libraries? 

Yes. Dual-indexed libraries may be used for both single-read and paired-end sequencing. Select the appropriate workflow based on the flow cell type (Single Read or Paired End) when starting your run so the correct chemistry is used. Please refer to Illumina’s Indexed Sequencing Overview Guide (15057455 v05) for details on dual indexed sequencing workflows on a single-read flow cell or a paired-end flow cell.