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.