Specifications for the NextSeq 1000/2000

Specifications for the NextSeq 1000 and 2000 systems.

Run Specifications Table 1: Sequencing Output Per Flow Cell

Flow Cell Type	P1\*	P2	P2 300 M††	P3\\
1 x 50 bp				60 Gb
2 x 50 bp	10 Gb	40 Gb		120 Gb
2 x 100 bp		80 Gb		240 Gb
2 x 150 bp	30 Gb	120 Gb		360 Gb
2 x 300 bp†	60 Gb		180 Gb
Single-End Reads Passing Filter	100 M	400 M	300 M	1.2 B
Paired-End Reads Passing Filter	200 M	800 M	600 M	2.4 B

Output specifications are based on a single flow cell using the Illumina PhiX control library.

Table 2: Quality Scores

| 1 x 50 bp | ≥ 90% of bases higher than Q30 at 1 x 50 bp | | 2 x 50 bp | ≥ 90% of bases higher than Q30 at 2 x 50 bp | | 2 x 100 bp | ≥ 85% of bases higher than Q30 at 2 x 100 bp | | 2 x 150 bp | ≥ 85% of bases higher than Q30 at 2 x 150 bp | | 2 x 300 bp† | ≥ 80% of bases higher than Q30 at 2 x 300 bp |

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.

Considerations when running 600 cycle P2 300 M read kits at read lengths <600 cycles (eg, 2x150 bp run with a 600 cycle kit)

• Q30: ≥ 80% Q30 new specification will apply for shorter runs. Kits that are less than 600 cycles will continue to use established ≥ 85% Q30 or ≥ 90% Q30 for each respective kits.

• Yield: If running the 600-cycle P2 kits at a total read length <600 cycles, expect yield based on the 300 M single-end reads/clusters specification, not yield based on the specifications for the 100-, 200-, and 300-cycle P2 kits. For example, a 2x150 cycle run performed with a P2 600-cycle kit can expect a yield of 90 Gb, compared to 120 Gb if the same run was performed with a P2 300-cycle kit.

Table 3: Run Time

Flow Cell Type	P1\*	P2	P3\\
1 x 50 bp			~11 hours
2 x 50 bp	~10 hours	~13 hours	~19 hours
2 x 100 bp		~21 hours	~33 hours
2 x 150 bp	~19 hours	~29 hours	~48 hours
2 X 300 bp†	~34 hours	~44 hours
Approximate time per cycle	2.8 min	4.8 min	8.5 min

Run time includes cluster generation, sequencing, and base calling on a NextSeq 1000 or NextSeq 2000 system.

NextSeq 1000/2000 control software version 1.5 of the NextSeq 1000/2000 Control Software introduces compatibility with the new 600-cycle P1 and P2 kits; older versions of the control software are not compatible.

\P1 flow cells require NextSeq 1000/2000 control software version 1.4 or greater. \\*P3 flow cells are available for the NextSeq 2000 only. † P1 and P2 600 cycle kits require NextSeq 1000/2000 control software version 1.5 †† 600 cycle kits guarantee 300 M reads because data quality over yield was prioritized and fewer tiles are imaged as compared to 100, 200, 300 cycle kits to achieve 400M reads.

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 non-condensing humidity.

  • Altitude: 0 meters - 2000 meters.

• Laser Wavelengths: 449 nm, 523 nm, 820 nm.

• Dimensions:

  • WxDxH: 60 cm x 65 cm x 60 cm.

  • Weight: 141 kg.

• Power Requirements:

  • Instrument Input Voltage: 100 Vac to 240 Vac.

  • 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.

See the NextSeq 1000 and NextSeq 2000 Specifications page for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #2387), contact Illumina Technical Support [e-mail].