Instruments

NextSeq 1000 and NextSeq 2000 Sequencing System specifications

Robust and proven benchtop sequencing

Scalable output, efficient runtimes, and high data quality

NextSeq 2000 in lab setting

Sequencing output per flow cella

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry

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. View standard SBS specifications here.
c. P3 and P4 reagents are available for the NextSeq 2000 System only.

Shelf life

NextSeq 1000 and NextSeq 2000 Sequencing Systems

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. View standard SBS specifications here.
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 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. View standard SBS specifications here.
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 P1 a P2 a P3 a,b P4 b
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. View standard SBS specifications here.
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

Application P1b P2b P3b,c P4c
  No. samples No. samples No. samples No. samples

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)d

50M read pairs per sample

 2d 8 24 36

mRNA-Seq (200 cycles)d

25M read pairs per sample

 4d 16 48 72

Single-cell RNA-Seq (100 cycles)e

5K cells, 20K reads per cell

 1e 4 12 48

miRNA-Seq or small RNA analysis (50 cycles)

11M reads per sample

 9f 36f 108f 163
16S RNA sequencing (600 cycles) 384g 384g N/A

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. View standard SBS specifications here.
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.

Instrument specifications

NextSeq 1k / 2k 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
    For Indoor Use Only
    Temperature: 15°C-30°C
    Humidity: 20%-80% relative humidity, non-condensing
    Altitude: 0 meters-2000 meters
  • Laser
    Wavelengths
    449 nm, 523 nm, 820 nm
  • Crated Dimensions
    W × D × H
    92 cm × 120 cm × 118 cm
    Weight: 232 kg
  • Dimensions
    W × D × H
    55 cm × 65 cm × 60 cm
    (21.7 in × 25.6 in × 23.6 in)
  • Weight
    141 kg (310.9 lb)
  • Crated weight
    232 kg (511.5 lb)
  • 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
View in-depth specs sheet (PDF)

Key technologies

XLEAP-SBS chemistry

The NextSeq 1000 and NextSeq 2000 Systems are powered by XLEAP-SBS chemistry, a faster, higher quality, and more robust SBS chemistry built on the proven foundation of standard Illumina SBS chemistry.* XLEAP-SBS nucleotides use state-of-the-art dyes and novel linkers and blocks that are more resistant to heat, show a 50× reduction in hydrolysis, and 2.5× faster block cleavage to reduce phasing and prephasing. The XLEAP-SBS polymerase is engineered to incorporate nucleotides faster and with higher fidelity than ever before.

*XLEAP-SBS chemistry on P1, P2, P3 will be available Q2 2024.

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. The technology supports massively parallel sequencing using a proprietary fluorescently labeled reversible terminator method. XLEAP-SBS chemistry on P1, P2, P3 will be available Q2 2024.

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.

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.