NextSeq 1000 and NextSeq 2000 Sequencing System specifications

Robust and proven benchtop sequencing

Scalable output, efficient runtimes, and high data quality

XLEAP-SBS Specification sheet

NextSeq 2000 in lab setting

Sequencing output per flow cell^a

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry

Flow cell type	P1^b	P2^b	P3^b,c	P4^c
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. 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 Life	P4 Shelf Life^a
Cartridge	-25°C to -15°C	6 months	3 months
Flow cell	2°C to 8°C	6 months	3 months
RSB with Tween 20^b	2°C to 8°C	6 months	6 months

a. In 1H of 2024, P4 shelf life will be 3 months. This will be extended to 6 months in 2H of 2024.
b. Shipped at room temperature.

Reads passing filter per flow cell

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry

Flow cell type	P1^a	P2^a	P3^a,b	P4^b
Single reads	100M	400M	1.2B	1.8B
Paired-end reads	200M	800M	2.4B	3.6B

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

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 Scores^c
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 Time^d
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. View standard SBS specifications here.
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 applications^a

NextSeq 1000 and NextSeq 2000 with XLEAP-SBS chemistry

Application	P1^b	P2^b	P3^b,c	P4^c
	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	~2^d	10	30	45
Total RNA-Seq (200 cycles) 50M read pairs per sample	2^d	8	24	36
mRNA-Seq (200 cycles) 25M read pairs per sample	4^d	16	48	72
Single-cell RNA-Seq (100 cycles) 5K cells, 20K reads per cell	1^e	4	12	48
miRNA-Seq or small RNA analysis (50 cycles) 11M reads per sample	9^f	36^f	108^f	163
16S RNA sequencing (600 cycles)	384^g	384^g

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. 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.

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.