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 Cell*

NextSeq 1000 and NextSeq 2000
Flow Cell Type P1 P2 P3
1 × 50 bp     60 Gb
2 × 50 bp 10 Gb 40 Gb 120 Gb
2 × 100 bp   80 Gb 240 Gb
2 × 150 bp 30 Gb 120 Gb 360 Gb
2 × 300 bp 60 Gb 180 Gb
(300 M)
 

* 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 system only.

Shelf Life

NextSeq 1000 and NextSeq 2000
Item Storage Temperature Shelf Life
Cartridge -25°C to -15°C 6 months
Flow Cell 2°C to 8°C 6 months
RSB with Tween 20* 2°C to 8°C 6 months

* Shipped at room temperature

Reads Passing Filter Per Flow Cell

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

* P3 Reagents are available for the NextSeq 2000 system only.
† 300M single-end reads for 2 × 300 bp.
600M paired-end reads for 2 × 300 bp.

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
2 × 300 bp ≥ 80% of bases higher than Q30 at 2 × 300 bp
Run Time  
1 × 50 bp     ~11 hr
2 × 50 bp ~10 hr ~13 hr ~19 hr
2 × 100 bp   ~21 hr ~33 hr
2 × 150 bp ~19 hr ~29 hr ~48 hr
2 × 300 bp ~34 hr ~44 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 system 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
Small Whole-Genome Sequencing (600 cycles)
130 Mb genome; > 30x coverage
~12 ~36
Whole-Exome Sequencing (200 cycles)
50× mean targeted coverage; 90% targeted coverage at 20×
~4 ~16 ~48
Total RNA-Seq (200 cycles) §
50M read pairs per sample
~2 ~16 ~24
mRNA-Seq (200 cycles) §
25M read pairs per sample
~4 ~32 ~48
Single-Cell RNA-Seq (100 cycles)**
5K cells, 20K reads/cell
1†† ~4 ~11
miRNA-Seq or Small RNA Analysis (50 cycles)
11M reads/sample
~9‡‡ 36§§ ~108
16S RNA sequencing (600 cycles) ~384*** ~384***

* Table values represent estimated number of samples per run.
P3 Reagents are available for the NextSeq 2000 system only.
Use P1 300-cycle kit.
§ Recommended read lengths are 2 × 75 bp for Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep and 2 × 100 bp for Illumina RNA Prep with Enrichment.
** Recommended sequencing depth will largely depend on sample type and experimental objective and will need to be optimized for each study.
†† P1 reagents are a good option for single-cell quality control experiments.
‡‡ Use P1 100-cycle kit.
§§ Use P2 100-cycle kit.
*** 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: 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 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 while maintaining the same high standards of data quality enjoyed by NextSeq 550 System users today.

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 while maintaining the same high standards of data quality enjoyed by NextSeq 550 System users today.

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.

Learn More

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.

Learn More

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.

Learn More

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

Contact Us