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Scalability for sequencing like never before

The NovaSeq 6000 System empowers new levels of possibilities, with unprecedented throughput

NovaSeq System Specifications

Sequencing Output Per Flow Cell

  NovaSeq 6000 System
Flow Cell Type SP* S1 S2 S4
2 × 50 bp 65–80 Gb 134–167 Gb 333–417 Gb N/A ‡
2 × 100 bp N/A ‡ 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.
‡ N/A: not applicable

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 SP  S1 S2 S4
Quality Scores  
2 × 50 bp ≥ 85%
2 × 100 bp ≥ 80%
2 × 150 bp ≥ 75%
2 x 250 bp ≥ 75%
Run Time  
2 × 50 bp ~13 hr ~13 hr ~16 hr N/A
2 × 100 bp N/A ~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 Series Specification Sheet

NovaSeq 6000 System Specification Sheet

The NovaSeq 6000 Sequencing System 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 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.

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See Patterned Flow Cells in Action