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.
‡ 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 (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 |
* 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 6000 System Specification Sheet
The NovaSeq 6000 System offers scalable throughput and flexibility for virtually any sequencing method, genome, and scale. Explore additional instrument specifications, supporting data, and other system details.
View Specification SheetKey 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.
See How SBS WorksPatterned 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.
See Patterned Flow Cells in ActionIllumina Reaches Milestone with 1,000 NovaSeq 6000
Three years after its debut, NovaSeq makes deeper discoveries more accessible than ever. The 1000th sequencer was placed at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts in June 2020.
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