Before preparing libraries, record information about your samples using an option available for your sequencing system.
After library preparation, denature and dilute libraries to the appropriate loading concentration using instructions for standard normalized libraries.
Follow the PhiX preparation instructions in the denature and dilute guides. Use a low-concentration PhiX spike-in (1%) as a positive control for alignment calculations and quantification efficiency.
To sequence TruSight Cardio libraries, set up a single-indexed paired-end run of 151 cycles for Read 1 and Read 2. Although a longer run is possible on the MiSeq, more than 151 cycles increases the likelihood of sequencing into the adapter sequences.