The NovaSeq 6000 combines 2 color SBS chemistry with the nanowell patterned flow cell. There are four flow cells options, SP, S1, S2, and the S4. There are two different ways to load the Flow cell, individual lane loading (XP) so as to run various experiments on the same flow cell or whole flow cell loading for one experiment across all lanes for greater coverage. The DNA Sequencing core has tested Whole Genomes on the NovaSeq as a way to bring back Whole Genome sequencing to the University. The DNA Sequencing core has also tested 10X Genomics Chromium RNA 3-Prime, WGBS, and Ribo depleted stranded RNA on the NovaSeq. We have compiled Illumina specifications for the NovaSeq in the tables below. To see a list of common and compatible sequencing methods for the NovaSeq 6000 visit Illumina’s website or reach out to the DNA Sequencing core for help with your project.


Flow cell Type Lanes per Flow Cell Read length (cycles) Output Quality Scores Run Time
SP** 2 50bp PE (100 cycles) 65-80 GB ≥85% ~13 hr
2 150bp PE (300 cycles) 200-250 Gb ≥75% ~25 hr
S1 2 50bp PE (100 cycles)     134-167 Gb ≥85% ~13 hr
  2 100bp PE (200 cycles) 266-333 Gb ≥80% ~19hr
  2 150bp PE (300 cycles) 400-500 Gb ≥75% ~25hr
S2 2 50bp PE (100 cycles) 333-417 Gb ≥85% ~16hr
  2 100bp PE (200 cycles) 667-833 Gb ≥80% ~25hr
  2 150bp PE (300 cycles) 1000-1250 Gb ≥75% ~36hr
 S4 100bp PE (200 cycles) 1600-2000Gb ≥80%  ~36hr
  4 150bp PE (300 cycles) 2400-3000 Gb ≥75% ~45hr

* specifications based on Illumina PhiX control library at supported cluster densities

*quality score is the percentage of bases >Q30 is average across the entire run. Quality scores are based on NovaSeq reagent kits run on the NovaSeq 6000 using Illumina PhiX control library. Performance may vary based on library type, quality, insert size, loading concentration and other experimental factors.

*run time is based on running two flow cells of the same type

** SP reagents have not been released yet, therefore performance metrics are subject to change


Flow cell Type SP** S1 S2 S4
Single End Reads 650-800 million 1.3-1.6 billion 3.3-4.1 billion 8-10 billion
Paired End Reads 1.3-1.6 billion 2.6-3.2 billion 6.6-8.2 billion 16-20 billion


Estimated Sample Throughput      
Flow cell Type SP** S1 S2 S4
Human Genomes per Run ~4 ~8 ~16 ~48
Exomes per Run ~40 ~80 ~200 ~500 
Transcriptomes per Run ~32 ~64 ~164 ~400 

* all sample throughput are estimates and are based on dual flow cell runs.

** SP reagents have not been released yet, therefore performance metrics are subject to change