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NovaSeq System Specifications

Immense discovery power for deeper insights

See the specifications for the NovaSeq 6000 system, our most powerful instrument for high-throughput sequencing

Sequencing Output Per Flow Cell*

NovaSeq 6000 System
Flow Cell Type SP S1 S2 S4
1 × 35 bp N/A N/A N/A 280-350 Gb
2 × 50 bp 65–80 Gb 134–167 Gb 333–417 Gb N/A
2 × 100 bp 134–167 Gb 266–333 Gb 667–833 Gb 1600–2000 Gb
2 × 150 bp 200–250 Gb 400–500 Gb 1000–1250 Gb 2400–3000 Gb
2 x 250 bp 325-400 Gb N/A N/A N/A

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

Reads Passing Filter Per Flow Cell

NovaSeq 6000 System
Flow Cell Type SP S1 S2 S4
Single-end Reads 650–800 M 1.3–1.6 B 3.3 B–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* and Run Time

NovaSeq 6000 System
Flow Cell Type
v1.5 Reagent Kits
SP S1 S2 S4
Quality Scores  
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 × 250 bp ≥ 75% of bases higher than Q30 at 2 × 250 bp
Run Time  
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 × 250 bp ~38 hr N/A N/A N/A
Flow Cell Type
v1.0 Reagent Kits
SP S1 S2 S4
Quality Scores  
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 × 250 bp ≥ 75% of bases higher than Q30 at 2 × 250 bp
Run Time  
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 × 250 bp ~38 hr N/A N/A N/A

* A quality score (Q-score) is a prediction of the probability of an error in base calling. The percentage of bases > Q30 is averaged across the entire run. Quality scores are based on NovaSeq Reagent Kits run on the NovaSeq 6000 System using an Illumina PhiX control library. Performance may vary based on library type and quality, insert size, loading concentration, and other experimental factors.
† 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 will impact run time.

Estimated Sample Throughput for Key Applications*

NovaSeq 6000 System
Flow Cell Type SP S1 S2 S4
Human Genomes per Run ~4 ~8 ~20 ~48
Exomes per Run ~40 ~80 ~200 ~500
Transcriptomes per Run ~32 ~64 ~164 ~400

*All sample throughputs are estimates and are based on dual flow cell runs. Human Genomes assumes > 120 Gb of data per sample to achieve 30× genome coverage. Exome assumes ~8Gb/100×. Transcriptomes assume ≥ 50M reads. Throughput may vary based on library preparation kit used.

NovaSeq Specifications

Instrument configuration
  • Computer and touch screen display
  • Installation setup and accessories
  • Data collection and analysis software
Instrument control computer
  • Base Unit: Portwell WADE-8022 with Intel i7 4700EQ CPU
  • Memory: 2 × 8 GB DDR3L SODIMM
  • Hard Drive: None
  • Solid-State Drive: 256 GB mSATA
  • Operating System: Windows 10
  • Note: Computer configurations will be upgraded regularly; contact your local account manager for current configuration
Operating environment
  • Temperature: 19°C-25°C (22°C ±3°C), <2°C change per hour
  • Humidity: 20%-80% relative humidity, non-condensing
  • Altitude: Below 2000 meters (6500 feet)
  • Ventilation: Maximum of 8530 BTU/h and average 6000 BTU/h
  • For Indoor Use Only
Laser
  • Wavelengths: 532 nm, 660 nm, 780 nm, 790 nm
Dimensions
  • W × D × H: 80.0 cm (31.5 in) × 94.5 cm (37.2 in) × 165.6 cm (65.2 in) with monitor
  • Weight: 481 kg (1059 lb), includes 3.5 kg (7.8 lb) for leak tray and 0.9 kg (2 lb) for keyboard and mouse, Crated Weight: 628 kg (1385 lb)
Crated Dimensions
  • Crated W×D×H: 92 cm × 120 cm × 118 cm
  • Crated Weight: 232 kg
Power requirements
  • 200–240 VAC 50/60Hz, 16A, single phase, 2500 W
  • Illumina provides a region-specific uninterruptible power supply
Network connection
  • Dedicated 1 Gb connection between the instrument and data management system. Connect directly or through network
Bandwidth for network connection
  • 200 Mb/s/instrument for internal network uploads
  • 200 Mb/s/instrument for BaseSpace Sequence Hub uploads
  • 5 Mb/s/instrument for Instrument Operational Data uploads
Download Specifications PDF
novaseq 6000 system drawing

Key Technology

Sequencing by Synthesis Technology

The NovaSeq 6000 System leverages proven Illumina sequencing by synthesis (SBS) technology to deliver accurate data and robust performance. SBS chemistry uses reversible-terminator fluorescently labeled nucleotides. This method detects single bases as they are incorporated into growing DNA strands, reading billions of sequences in parallel.

Learn More

See How SBS Works

Patterned Flow Cell Technology

The NovaSeq 6000 System incorporates patterned flow cell technology to generate an unprecedented level of throughput for a broad range of sequencing applications. Patterned flow cells contain billions of nanowells at fixed locations, a design that provides even spacing of sequencing clusters. This delivers significant increases in sequencing reads and total output of the system.

Learn More

See Patterned Flow Cells in Action

Interested in learning more about the power of NovaSeq? Talk to an Illumina representative today.

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