Question: Can I use a 100-cycle NovaSeq kit to sequence Visium libraries?
Answer: This depends on the library type and the NovaSeq Reagent Kit version.
Illumina currently offers two versions of NovaSeq Reagent Kits (for SP, S1, and S2 flow cells):
- The 100-cycle NovaSeq v1 Reagent Kit contains an additional 30 cycles of reagents, allowing for a maximum of 130 total cycles.
- The 100-cycle NovaSeq v1.5 Reagent Kit contains an additional 38 cycles of reagents, allowing for a maximum of 138 total cycles. This kit was released in August 2020.
Additional details regarding the cycle numbers in the different Illumina reagent kits can be found on the Illumina website: How many cycles of SBS chemistry are in my kit?
Visium for fresh-frozen and Visium for FFPE libraries require different sequencing parameters:
- Visium for fresh-frozen
- Visium libraries from fresh-frozen tissues require 138 cycles (R1 28, i7 10, i5 10, R2 90) for sequencing. The NovaSeq v1.5 Reagent Kit contains sufficient reagents to sequence these libraries at our recommended read lengths.
- However, the NovaSeq v1 Reagent Kit only contains enough reagents for 130 cycles, which is insufficient to sequence Visium for fresh-frozen libraries at our recommended read lengths. Read 2 cycle number would need to be reduced to accommodate the capacity of this kit, which may lead to decreased mapping rates.
- Visium for FFPE
- Visium for FFPE libraries requires 98 cycles (R1 28, i7 10, i5 10, R2 50) for sequencing. The NovaSeq 100-cycle v1 and v1.5 Reagent Kits contain sufficient reagents to sequence these libraries at our recommended read lengths.
Products: Visium for fresh-frozen, Visium for FFPE