Question: What sequencing parameters should be used for Visium libraries?
Answer: Visium libraries should be run paired-end, dual index configuration. We recommend the following sequencing cycling conditions:
Read 1 - 28 cycles
i5 index - 10 cycles
I7 index - 10 cycles
Read 2 - 120 cycles
We do not recommend shortening Read 2. Reducing the cycle number for Read 2 to accommodate a 100 cycle sequencing kit (75 cycles) has shown ~15% decrease in assay sensitivity.