Specifications for the NovaSeq 6000

Q30 Specifications for v1 vs v1.5 reagent kits

Cycles	Q30 NovaSeq 6000 v1**.0**(SP/S1/S2/S4)	Q30NovaSeq 6000 v1.5(SP/S1/S2/S4)
1 x 35 bp	N/A	≥ 90%
2 × 50 bp	≥ 85%	≥ 90%
2 × 100 bp	≥ 80%	≥ 85%
2 × 150 bp	≥ 75%	≥ 85%
2 x 250 bp	≥ 75%	≥ 75%

**Performance Parameters for NovaSeq 6000 v1.5 Reagent Kits

Total Expected Output for v1.5 Reagent Kits**

Output	Flow Cell Types
	SP
1 × 35 bp	N/A
2 × 50 bp	65-80 Gb
2 × 100 bp	134-167 Gb
2 × 150 bp	200-250 Gb
2 × 250 bp	325-400 Gb
Single read Passing Filter	650-800 M
Paired-end Passing Filter	1.3-1.6 B

\*Specifications based on Illumina PhiX control library at supported cluster densities.

Quality Scores for v1.5 Reagent Kits

Run Configuration	Quality scores
(Kit type)
1 × 35 bp	≥ 90% of bases higher than Q30 at 1 × 35 bp
2 × 50 bp	≥ 90% of bases higher than Q30 at 2 × 50 bp
2 × 100 bp	≥ 85% of bases higher than Q30 at 2 × 100 bp
2 × 150 bp	≥ 85% of bases higher than Q30 at 2 × 150 bp
2 x 250 bp	≥ 75% of bases higher than Q30 at 2 × 250 bp

Run time estimate for v1.5 Reagent Kits

| Run Time\* | SP | S1 | S2 | S4 | | 1 × 35 bp | N/A | N/A | N/A | ~14 hr | | 2 × 50 bp | ~13 hr | ~13 hr | ~16 hr | N/A | | 2 × 100 bp | ~19 hr | ~19 hr | ~25 hr | ~36 hr | | 2 × 150 bp | ~25 hr | ~25 hr | ~36 hr | ~44 hr | | 2 x 250 bp | ~38 hr | N/A | N/A | N/A |

\*Note: Run time includes cluster generation, sequencing, and base calling. Run times are based on running 2 flow cells of the same type; starting two different flow cells (lower and higher throughput) will impact run time.

For further information on run time estimates, search for Knowledge Base article Run time estimates for each sequencing step on the Illumina sequencing platform

Performance Parameters for NovaSeq 6000 v1.0 Reagent Kits

Total Expected Output for v1.0 Reagent Kits

Output	Flow Cell Types
	SP
2 × 50 bp	65-80 Gb
2 × 100 bp	134-167 Gb
2 × 150 bp	200-250 Gb
2 × 250 bp	325-400 Gb
SR Passing Filter	650-800 M
PE Passing Filter	1.3-1.6 B

\*Specifications based on Illumina PhiX control library at supported cluster densities.

Quality Scores for v1.0 Reagent Kits

Run Configuration	Quality scores
(Kit type)
2 × 50 bp	≥ 85% of bases higher than Q30 at 2 × 50 bp
2 × 100 bp	≥ 80% of bases higher than Q30 at 2 × 100 bp
2 × 150 bp	≥ 75% of bases higher than Q30 at 2 × 150 bp
2 x 250 bp	≥ 75% of bases higher than Q30 at 2 × 250 bp

Run time estimate for v1.0 Reagent Kits

| Run Time\* | SP | S1 | S2 | S4 | | 2 × 50 bp | ~13 hr | ~13 hr | ~16 hr | N/A | | 2 × 100 bp | ~19 hr | ~19 hr | ~25 hr | ~36 hr | | 2 × 150 bp | ~25 hr | ~25 hr | ~36 hr | ~44 hr | | 2 x 250 bp | ~38 hr | N/A | N/A | N/A |

\*NOTE: Run time includes cluster generation, sequencing, and base calling. Run times are based on running 2 flow cells of the same type; starting two different flow cells (lower and higher throughput) will impact run time.

For further information on run time estimates, search for Knowledge Base article Run time estimates for each sequencing step on the Illumina sequencing platform

See the NovaSeq 6000 System Specifications page for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #2669), contact Illumina Technical Support [e-mail].