NextSeq 1000 & NextSeq 2000 Systems


75 breakthrough innovations in one powerful instrument.

Science moves fast, and so do you. Access applications like single-cell, whole exome, and RNA sequencing, preparing for the future today.

Easier than ever. Accelerated decision making.

Experience our simplest workflow yet with dry instrumentation, easier run set up and DRAGEN on-board for 6x faster secondary analysis. Now with lossless genomic compression, saving up to 80% on storage costs.

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See the system in your lab

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Sequencing power for the applications you need

NextSeq 2000 is redesigned from the ground up to maximize future proofing, offering sequencing power for high throughput applications. Offering scalability for evolving needs and larger studies, it supports a vast variety of applications, including:

Single-Cell Gene Expression

(100 cycles) 4k cells; 10k-50k reads/cell*

Examine the transcriptomes of individual cells for a high-resolution view of cell-to-cell variation. Explore the distinct biology of individual cells in complex tissues and understand cellular subpopulation responses to environmental cues. With P2 reagents, analyze 2-10 samples in approximately 13 hours. Or step up to P3 reagents to analyze 6-30 samples in approximately 19 hours.

*Recommended sequencing depth will largely depend on sample type and experimental objective and will need to be optimized for each study.

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Whole-Exome Sequencing

(200 cycles) 50× mean target coverage

Exome sequencing is a cost-effective approach when whole-genome sequencing is not practical or necessary. Efficiently identify coding variants across a broad range of applications, including population genetics, genetic disease, and cancer studies. In about 19 hours you can analyze 4 samples with P1 reagents. Or scale up to 16 samples in approximately 21 hours with P2 reagents, or 48 samples in approximately 33 hours with P3 reagents.

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Shotgun Metagenomics

(300 cycles) 50M reads/sample

Comprehensively sample all genes in all organisms present in a given complex sample. Evaluate bacterial diversity and detect the abundance of microbes in various environments or study unculturable microorganisms that are otherwise difficult or impossible to analyze. You can analyze 2 samples in about 19 hours with P1 reagents or step up to 8 samples in about 29 hours with P2 reagents. Scale up to 24 samples in approximately 48 hours with P3 reagents.

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Expand Your Access to More Data and Applications

High-Throughput Sequencing

Probe deeper into a single sample for insights or process more samples to improve statistical signficance.


Perform transformative science with access to multiple emerging high-throughput omics applications.

Efficient and Cost-Effective

Researchers talk about their experience using the NextSeq 1000 and NextSeq 2000 Sequencing Systems.

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Efficient and Cost-Effective

System Specifications

30-360 Gb*
output range
100 M-2.4 B**
reads per run
2 x 150 bp
max read length

*Specifications based on Illumina PhiX control library at supported cluster densities.
**100 M - 1.2 B single reads per run. 200 M - 2.4 B paired-end reads per run.


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