NextSeq 1000 & NextSeq 2000 Systems


Unlock a broad range of applications with one powerful instrument

Science moves fast, and so do you. Access applications ranging from targeted sequencing to data-rich multiomics applications including whole-exome, spatial transcriptomics, and single-cell sequencing. Scalability to help you prepare for the future today.

NextSeq with DRAGEN

Accelerated discovery. Easier than ever.

Experience our simplest workflow yet with easier run setup, time-saving dry instrumentation, and DRAGEN on-board for no additional cost, providing accurate and efficient secondary analysis, up to 6x faster. Now with losless genomic compression, saving up to 80% on storage costs.

Learn More

See the system in your lap

See the system in your lab

Frame the QR code with your smartphone for a virtual view of the system on-location in your lab environment.

QR code: Simulate the system on-location in your lab environment

Sequencing flexibility for the applications you need

The NextSeq 1000 and NextSeq 2000 are redesigned from the ground up. Their flexibility, affordability, and scalability help both new and experienced users achieve fast turnaround times and reduced operating costs. With the wide range of available flow cells, they support a variety of applications including:

Single-Cell Gene Expression

Examine the transcriptomes of individual cells for a high-resolution view of cell-to-cell variation.

Whole-Exome Sequencing

Efficiently identify coding variants across a broad range of applications, including population genetics, genetic disease, and cancer studies.

Shotgun Metagenomics

Comprehensively sample all genes in all organisms present in a given complex sample.

Spacial Transcriptomics

Pinpoint predictive cellular state and their spatial localization to understand the influence of the cellular and spatial architecture on the microenvironment.

Total RNA Sequencing

Analyze both coding RNA and multiple forms of noncoding RNA for a comprehensive view of the transcriptome.

Infectious Disease Research

Infectious Disease Research Description: A universal, culture-free method for infectious disease characterization and surveillance that may be used with viruses, bacteria, fungi, and parasites, and can replace the need for multiple tests.

Expand Your Access to More Data and Applications

High Intensity Sequencing

High-intensity sequencing applications generate dramatically more data for more impactful insights.


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.

View Video
Efficient and Cost-Effective

System Specifications

10-360 Gb*
output range
100 M-2.4 B**
reads per run
2 x 300 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.

The NextSeq 1000 runs P1 and P2 flow cells, offering fast turnaround times, lower throughput, and a lower cost instrument. The NextSeq 2000 accesses a wider range of throughputs with P1, P2, and P3 flow cells for more sequencing per sample, larger studies, and better run economics.
Both systems use patterned flow cells to offer the highest cluster density flow cell of any on-market NGS system to date, driving down the run cost. In these flow cells, monitoring the Cluster PF (%) is a better measure of potential cluster occupancy than measuring cluster density..
Upgrading from a NextSeq 1000 instrument to a NextSeq 2000 instrument is seamless. Contact us for more information.

Recommended Products


Interested in speaking to a specialist about the NextSeq 1000 and NextSeq 2000 Systems?

Contact us.

Contact us.