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NextSeq 1000 & NextSeq 2000 Specifications

Scale for the future while driving efficiencies today

See the specifications for NextSeq 1000 and 2000 systems, redesigned from the ground up for evolving needs

Sequencing Output Per Flow Cell*

NextSeq 1000 and NextSeq 2000
Flow Cell Type P1 P2 P3
1 × 50 bp     60 Gb
2 × 50 bp   40 Gb 120 Gb
2 × 100 bp   80 Gb 240 Gb
2 × 150 bp 30 Gb 120 Gb 360 Gb

* Output specifications based on a single flow cell using Illumina PhiX control library at supported cluster densities.
† P3 Reagents are available for the NextSeq 2000 only.

Reads Passing Filter Per Flow Cell

NextSeq 1000 and NextSeq 2000
Flow Cell Type P1 P2 P3 *
Single-end Reads 100 M 400 M 1.2 B
Paired-end Reads 200 M 800 M 2.4 B

* P3 Reagents are available for the NextSeq 2000 only.

Quality Scores* and Run Time

NextSeq 1000 and NextSeq 2000
Flow Cell Type P1 P2 P3
Quality Scores  
1 × 50 bp ≥ 90% of bases higher than Q30 at 1 × 50 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
Run Time  
1 × 50 bp     ~11 hr
2 × 50 bp   ~13 hr ~19 hr
2 × 100 bp   ~21 hr ~33 hr
2 × 150 bp ~19 hr ~29 hr ~48 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. Quality scores are based on NextSeq Reagent Kits run on the NextSeq 1000 and 2000 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 on a NextSeq 1000 or NextSeq 2000 system.
‡ P3 Reagents are available for the NextSeq 2000 only.

Estimated Sample Throughput for Key Applications

NextSeq 1000 and NextSeq 2000
Flow Cell Type P1 P2 P3 *
Small Whole-Genome Sequencing (300 cycles)
130 Mb genome; > 30× coverage
~7 ~30 ~90
Whole-Exome Sequencing (200 cycles)
50× mean targeted coverage; 90% targeted coverage at 20×
~4 ~16 ~48
Single-Cell RNA-Seq (100 cycles)
4k cells, 10k-50k reads/cell
  ~2-10 ~6-30
miRNA-Seq or Small RNA Analysis (50 cycles)
11M reads/sample
    ~108

* P3 Reagents are available for the NextSeq 2000 only.
† Recommended sequencing depth for single-cell RNA-Seq will largely depend on sample type and experimental objective and will need to be optimized for each study.

NextSeq 1000 and NextSeq 2000
Specifications

Instrument configuration
  • Self-contained, dry instrument with integrated DRAGEN Bio-IT FPGA secondary analysis
Instrument control computer
  • Base Unit: 2U Microserver located inside the instrument
  • Memory: 288 GB
  • Hard Drive: 3.8 TB SSD
  • Operating System: Linux CentOS 7.6
Operating environment
  • Temperature: 15°C-30°C
  • Humidity: 20%-80% relative humidity, non-condensing
  • Altitude: 0 meters-2000 meters
  • For Indoor Use Only
Laser
  • Wavelengths: 449 nm, 523 nm, 820nm
Dimensions
  • W×D×H: 60 cm × 65 cm × 60 cm
  • Weight: 141 kg
Crated Dimensions
  • Crated W×D×H: 92 cm × 120 cm × 118 cm
  • Crated Weight: 232 kg
Power requirements
  • Instrument Input Voltage: 100Vac to 240Vac
  • Instrument Input Frequency: 50/60Hz
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
Product safety and compliance
  • Safety: Class 1 Laser Product
  • NRTL certified IEC
  • 61010-1 CE marked
  • FCC/IC approved
Download Specifications PDF
nextseq 2000 system drawing

NextSeq 1000 and NextSeq 2000
Cartridge

Easy-to-use cartridge-based platform

The NextSeq 1000 and NextSeq 2000 Sequencing Systems take advantage of an integrated cartridge that includes reagents, fluidics, and the waste holder, simplifying library loading and instrument use. Simply thaw the reagent cartridge, insert the flow cell into the cartridge, load the library into the cartridge, and insert the assembled cartridge into the instrument.

NextSeq 1000 and NextSeq 2000
Flow Cell

Increased output

To take full advantage of higher density flow cells, the NextSeq 1000 and NextSeq 2000 Sequencing Systems feature a novel super resolution optics system that yields highly accurate imaging data with greater resolution and higher sensitivity than traditional benchtop systems. This miniaturization provides scalability for a variety of output quantities while maintaining the same high standards of data quality enjoyed by NextSeq 550 System users today.

NextSeq 2000 Cartidge
NextSeq 2000 Flow Cell

NextSeq 1000 and NextSeq 2000
Flow Cell

Increased output

To take full advantage of higher density flow cells, the NextSeq 1000 and NextSeq 2000 Sequencing Systems feature a novel super resolution optics system that yields highly accurate imaging data with greater resolution and higher sensitivity than traditional benchtop systems. This miniaturization provides scalability for a variety of output quantities while maintaining the same high standards of data quality enjoyed by NextSeq 550 System users today.

Interested in learning more about the flexibility of NextSeq 1000/2000? Talk to an Illumina representative today.

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