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Scalability for sequencing like never before

The NovaSeq Series empowers new levels of possibilities, with unprecedented throughput

NovaSeq System Specifications

Sequencing Output per Flow Cell

  NovaSeq 5000 and 6000 Systems NovaSeq 6000 System
Flow Cell Type S1* S2 S3* S4*
2 × 50 bp up to 167 Gb 280–333 Gb NA** NA**
2 × 100 bp up to 333 Gb 560–667 Gb NA** NA**
2 × 150 bp up to 500 Gb 850–1000 Gb up to 2000 Gb up to 3000 Gb

Specifications based on Illumina PhiX control library at supported cluster densities.
*The NovaSeq 5000 System, NovaSeq 5000 System Upgrade, and NovaSeq Reagent Kits with S1, S3, or S4 flow cells are not currently available for order.
** NA: not applicable

Reads Passing Filter

  NovaSeq 5000 and 6000 Systems NovaSeq 6000 System
Flow Cell Type S1* S2 S3* S4*
  up to 1.6 B 2.8–3.3 B up to 6.6 B up to 10 B

Quality Scores† and Run Time††

  NovaSeq 6000 System
Flow Cell Type S2
Read Length 2 × 50 bp 2 × 100 bp 2 × 150 bp
Quality Score (percent of bases above Q30) ≥ 85 % ≥ 80 % ≥ 75 %
Run Times 19 hr 29 hr 40 hr

† 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.
†† Run time includes cluster generation, sequencing, and base calling for a dual S2 flow cell run on the NovaSeq 6000 System.

Estimated Sample Throughput for Key Applications†††

  NovaSeq 5000 and 6000 Systems NovaSeq 6000 System
Flow Cell Type S1* S2 S3* S4*
Human Genomes per Run up to 8 up to 16 up to 32 up to 48
Exomes per Run up to 66 up to 132    
Transcriptomes per Run up to 66 up to 132    

††† 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. Exomes assumes ≥ 50M reads at ≥ 2 × 75 bp. Transcriptomes assumes ≥ 50M reads at ≥ 2 × 50 bp.

NovaSeq Series Specification Sheet

NovaSeq Series Specification Sheet

The NovaSeq Series of Sequencing Systems offers scalable throughput and flexibility for virtually any sequencing method, genome, and scale. Complete projects faster and more economically than ever before—and redefine the limits of your research.

View Specification Sheet

Key Technology

Sequencing by Synthesis Technology

The NovaSeq 5000 and NovaSeq 6000 Systems leverage 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 Series 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