Question: Can I use the 100-cycle NovaSeq kit for Single Cell 3' and 5' assays?
Answer: This depends on the library type and the NovaSeq Reagent Kit version.
Illumina currently offers two versions of the 100 cycle 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
Single and dual index libraries require different sequencing parameters:
- Single index
- For single index 3' Gene Expression v3/v3.1 libraries and single index 5' Gene Expression v1/v1.1 libraries, the NovaSeq 100-cycle v1 and v1.5 Reagent Kits contain sufficient reagents to sequence these libraries at our recommended read lengths
- Dual index
- For dual index 3' Gene Expression v3.1, dual index 3' Gene Expression LT v3.1, and dual index 5' Gene Expression v2 libraries, 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 not sufficient to sequence dual index 3' or 5' libraries at our recommended read lengths. Read 2 would need to be shortened to accommodate this kit, which may lead to decreased mapping rates. See: Can I decrease the sequencing length of Read 2 for Single Cell Gene Expression assays?
Products: Single Cell Gene Expression, Single Cell Immune Profiling