Instruments

NovaSeq 6000 Sequencing System specifications

Powerful performance at hand

Scalable, high-throughput sequencing with tunable output

NovaSeq 6000 system render

Output per flow cell for various read lengthsa

Read length 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 × 250 bpb 325-400 Gb N/A N/A N/A

a. Output specifications based on Illumina PhiX control library at supported cluster densities. NovaSeq 6000 system is capable of single flow cell runs or dual flow cell runs. Dual flow cell run delivers twice the output listed above. ​

b. Maximum read length.

Estimated sample throughput for key applicationsa

Application 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

a. 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 ~8 Gb/100×. Transcriptomes assume ≥ 50M reads. Throughput may vary based on library preparation kit used.

Reads passing filter per flow cella

Read type SP S1 S2 S4
Single-end reads 650–800M 1.3–1.6B 3.3–4.1B 8–10B
Paired-end reads 1.3–1.6B 2.6–3.2B 6.6–8.2B 16–20B

a. 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 ~8 Gb/100×. Transcriptomes assume ≥ 50M reads. Throughput may vary based on library preparation kit used.

Quality scoresa

Read length SP S1 S2 S4
1 × 35 bp N/A N/A N/A ≥ 90% of bases higher than Q30
2 × 50 bp ≥ 90% of bases higher than Q30 N/A
2 × 100 bp ≥ 85% of bases higher than Q30
2 × 150 bp ≥ 85% of bases higher than Q30
2 × 250 bp ≥ 75% of bases higher than Q30 N/A N/A N/A

a. Quality score based on NovaSeq 6000 Reagent Kits v1.5 using an Illumina PhiX control library.

Run timea

Read length 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 × 250 bp ~38 hr N/A N/A N/A

a. Run time based on NovaSeq 6000 Reagent Kits v1.5 using an Illumina PhiX control library while running two flow cells simultaneously.

Instrument specifications

NovaSeq 6000 system specifications

NovaSeq 6000 instrument specifications

  • Instrument configuration
    Computer and touch screen display Installation setup and accessories data collection and analysis software
  • Instrument control computer
    Note: Computer configurations will be upgraded regularly; contact your local account manager for current configuration
    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
  • Operating environment
    For Indoor Use Only
    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
  • Laser
    Wavelengths
    532 nm, 660 nm, 780 nm, 790 nm
  • Dimensions with monitor
    W × D × H
    80.0 cm × 94.5 cm × 165.6 cm
    (31.5 in × 37.2 in × 65.2 in)
  • 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 Dimensions
    W × D × H
    92 cm × 120 cm × 118 cm
  • Crated Weight
    628 kg (1385 lb)
  • 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
View in-depth specs sheet (PDF)

Key technologies

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.

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.