NextSeq 1000 & NextSeq 2000 Specifications

Scalable output, efficient runtimes, and high data quality

See the instrument specifications that make a wide range of applications possible

Sequencing output per flow cella

NextSeq 1000 and NextSeq 2000
Flow cell type P1b P2b P3b,c P4c
1 × 50 bp       90 Gb
2 × 50 bp 10 Gb 40 Gb 120 Gb 180 Gb
2 × 100 bp   80 Gb 240 Gb 360 Gb
2 × 150 bp 30 Gb 120 Gb 360 Gb 540 Gb
2 × 300 bp 60 Gb 240 Gb    

a. Output specifications are based on an Illumina PhiX control library at supported cluster densities.
b. XLEAP-SBS reagents for P1, P2, and P3 flow cells available Q2 of 2024.
c. P3 and P4 reagents are available for the NextSeq 2000 System only.

Shelf life

NextSeq 1000 and NextSeq 2000
Item Storage Temperature P1, P2, P3 Shelf Lifea P4 Shelf Lifeb
Cartridge -25°C to -15°C 6 months 3 months
Flow Cell 2°C to 8°C 6 months 3 months
RSB with Tween 20c 2°C to 8°C 6 months 6 months

a. P1, P2, and P3 with XLEAP-SBS chemistry will launch in Q2 of 2024 with a shelf life of 6 months.
b. In 1H of 2024, P4 shelf life will be 3 months. This will be extended to 6 months in 2H of 2024.
c. Shipped at room temperature.

Reads passing filter per flow cell

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry
Flow Cell Type P1a P2a P3a,b P4b
Single-end Reads 100M 400M c 1.2B 1.8B
Paired-end Reads 200M 800M d 2.4B 3.6B

a. XLEAP-SBS reagents for P1, P2, and P3 flow cells available Q2 of 2024.
b. P3 and P4 reagents are available for the NextSeq 2000 System only.
c. 300M single-end reads for 2 × 300 bp with standard SBS chemistry. 400M single-ends reads for 2 x 300 bp with XLEAP-SBS chemistry.
d. 600M paired-end reads for 2 × 300 bp with standard SBS chemistry. 800M single-ends reads for 2 x 300 bp with XLEAP-SBS chemistry.

Quality scores and run time

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry
Flow cell type P1a P2a P3a,b P4b
Quality scoresc
1 × 50 bp ≥ 90% of bases higher than Q30
2 × 50 bp ≥ 90% of bases higher than Q30
2 × 100 bp ≥ 90% of bases higher than Q30
2 × 150 bp ≥ 90% of bases higher than Q30
2 × 300 bp ≥ 85% of bases higher than Q30
Run timed
1 × 50 bp       12 hr
2 × 50 bp 8 hr 12 hr 18 hr 20 hr
2 × 100 bp   19 hr 31 hr 34 hr
2 × 150 bp 17 hr 22 hr 40 hr 44 hr
2 × 300 bp 34 hr 42 hr    

a. XLEAP-SBS reagents for P1, P2, and P3 flow cells available Q2 of 2024.
b. P3 and P4 reagents are available for the NextSeq 2000 System only.
c. Quality scores are based on an Illumina PhiX control library; performance may vary based on library type and quality, insert size, loading concentration, and other experimental factors.
d. Run time includes cluster generation, sequencing, and base calling on a NextSeq 1000 or NextSeq 2000 System.

Estimated sample throughput for key applicationsa

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry
Flow Cell Type P1b P2b P3b,c P4c
Small Whole-Genome Sequencing (300 cycles)
130 Mb genome; > 30× coverage
7 30 92 138
Whole-Exome Sequencing (200 cycles)
~8 Gb per exome, 90× mean coverage
~2d 10 30 45
Total RNA-Seq (200 cycles)
50M read pairs per sample
2d 8 24 36
mRNA-Seq (200 cycles)
25M read pairs per sample
4d 16 48 72
Single-Cell RNA-Seq (100 cycles)
5K cells, 20K reads/sample
1e 4 12 48
miRNA-Seq or Small RNA Analysis (50 cycles)
11M reads/sample
9f 36f 108f 163
16S RNA sequencing (600 cycles) 384g 384g    

a. Table values represent estimated number of samples per run. Recommended sequencing depth will largely depend on sample type and experimental objective and will need to be optimized for each study.
b. XLEAP-SBS reagents for P1, P2, and P3 flow cells available Q2 of 2024.
c. P3 and P4 reagents are available for the NextSeq 2000 System only.
d. Use P1 300-cycle kit.
e. P1 reagents are a good option for single-cell quality control experiments.
f. Use 100-cycle kits.
g. A maximum of 384 unique dual indexes is available from Illumina.

NextSeq 1000 and NextSeq 2000
Instrument 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: 55 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 and sustainable 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. After the run, use the recycling tool to separate multiple plastic components of the reagent cartridge for recycling according to local regulations.

View Reagents

NextSeq 1000 and NextSeq 2000
Flow Cell

Increased output, Decreased Operating expenses

To take full advantage of higher density flow cells, the NextSeq 1000 and NextSeq 2000 Sequencing Systems feature a novel super resolution optical 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.

View Data Concordance

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 optical 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.

Key Technology

Sequencing by Synthesis Technology

The NextSeq 1000 and 2000 systems leverage proven sequencing by synthesis (SBS) technology to to deliver highly accurate data and robust performance. SBS is the same proven technology used by all Illumina sequencing platforms. The technology supports massively parallel sequencing using a proprietary fluorescently labeled reversible terminator method. The NextSeq 2000 System is now powered by XLEAP-SBS chemistry with the new P4 flow cell.

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Patterned Flow Cell Technology

The NextSeq 1000 and 2000 systems utilize innovative patterned flow cell technology, which offers an exceptional level of throughput for diverse 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.

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Lossless Genomic Data Compression Technology

Lossless genomic compression is available on-instrument with the NextSeq 1000 and NextSeq 2000 Sequencing Systems. This technology uses an ultra-fast mapping scheme to map reads onto a reference genome, and then store only the data needed to regenerate those reads: a position and a list of differences.

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

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