Illumina NovaSeq 6000

The NovaSeq 6000 is our largest sequencing system, both in terms of output and size. It is very flexible as it offers four different flow cell types (SP, S1, S2 and S4) with a wide range of outputs and prices. The instrument is typically used for applications like Single Cell RNASeq, whole genome sequencing of large genomes and whole exome sequencing etc. The NovaSeq 6000 runs a dual flow cell system, meaning that two flow cells (A and B) can run simultaneously, either as one run or as two independent runs.

Specifications

Sequencing output per flow cell

	Flow cell type
Seq. kit	SP	S1	S2	S4
2x50 bp	65-80 Gb	134-167 Gb	333-417 Gb	NA
2x100 bp	NA	266-336 Gb	667-833 Gb	1600-2000 Gb
2x150 bp	200-250 Gb	400-500 Gb	1000-1250 Gb	2400-3000 Gb
2x250 bp	325-400 Gb	NA	NA	NA

Gb= Giga bases, NA=Not available

The outputs listed in the table above, should only be used as a guideline. As the final output of a sequencing run depends on the given sequencing library.

Reads passing QC filter per Flow cell

	Flow cell type
Read type	SP	S1	S2	S4
Single-end Reads	650-800	1,3-1,6 B	3,3-4,1 B	8-10 B
Paired-end Reads	1,3-1,6 B	2,6-3,2 B	6,6-8,2 B	16-20 B

Quality Scores

	Flow cell type
Seq. kit	SP	S1	S2	S4
2x50 bp	≥ 85% of bases higher than Q30
2x100 bp	≥ 80% of bases higher than Q30
2x150 bp	≥ 75% of bases higher than Q30
2x250 bp	≥ 75% of bases higher than Q30

The Q-Score predicts the probability of an error in the base calling. A Q-score of 30 is equal to a base call accuracy of 99, 9% or in other words an incorrect base call for 1 in a 1000 bases.

Runtimes

	Flow cell type
Seq. kit	SP	S1	S2	S4
2x50 bp	13 hours	13 hours	16 hours	NA
2x100 bp	NA	19 hours	25 hours	36 hours
2x150 bp	25 hours	25 hours	36 hours	44 hours
2x250 bp	38 hours	NA	NA	NA

The runtimes are only guidelines as they are based on running two flow cells of the same type. Running two different flow cells will impact the run times.