NextSeq 1000 and NextSeq 2000 Sequencing Systems

Advance your research

Proven technology to power your discovery

NextSeq 1000 and NextSeq 2000 Sequencing Systems

NextSeq 1000 and NextSeq 2000 in laboratory setting

Innovative sequencing for more biological discoveries

The NextSeq 1000 and NextSeq 2000 Systems are thoughtfully designed to enable more insights on your benchtop. With 14 configurations and read lengths from 1 × 50bp to 2 × 300bp, these systems efficiently handle benchtop workflows while driving down costs and minimizing waste. Confidently expand your research with the NextSeq 1000 and NextSeq 2000 Systems.

Robust performance powered by an intuitive workflow

These systems offer operational ease and onboard informatics, simplifying workflows for both new and advanced users. Advanced XLEAP-SBS chemistry, built on the proven foundation of standard Illumina SBS chemistry, enables faster, more economical, and higher quality sequencing than ever before.

scientist starting sequencing run on NextSeq 1k/2k

Delivering sequencing success through community

The NextSeq 1000 and NextSeq 2000 Systems offer the certainty of a field-tested solution and a reliable sequencing partner. Take advantage of a large ecosystem of applications, protocols, and informatics built in collaboration with thousands of researchers and thought leaders across the globe.

Experience the new P4 flow cell on NextSeq 2000

Expand your capabilities. Achieve 1.8 billion single-end reads per run to power the most data-intensive applications on your benchtop sequencer.

NextSeq 2000 System specifications

System specifications

Output range^a

10–540 Gb
Single-end reads per run

100M–1.8B
Max read length

2 × 300 bp
Run time

8–44 hr

a. Specifications based on Illumina PhiX control library at supported cluster densities.

View all NextSeq 1000 & 2000 specifications

Intuitive workflows from start to finish

With the help of the NextSeq 2000 and AI, Dyno Therapeutics is powering a new approach to gene therapy. Hear from Eric Kelsic and Ben Noyes about how they are accelerating drug discovery with innovative, scalable technologies.

Intuitive workflows from start to finish

The NextSeq 1000 and NextSeq 2000 Systems provide a comprehensive workflow that includes user-friendly run setup, a wide ecosystem of compatible library prep kits, load-and-go operation, and integrated, onboard secondary analysis.

Manage workflow

Track samples and manage runs easily and efficiently with cloud-based and on-premises options.

Prepare libraries

Prepare libraries with a wide range of compatible library preparation kits.

Sequence

Generate sequences with scalable output, efficient run times, and high data quality.

Analyze data

Analyze using onboard DRAGEN secondary analysis or stream to the cloud for additional analysis flexibility.

Interpret results

Access BaseSpace apps, instrument performance data, license management, and long-term storage solutions.

See why researchers choose Illumina

When you partner with Illumina, you’ll get more than just leading-edge technology–you become part of a community with like-minded goals.

Learn more

scientist adding solution to P4 flow cell

Superior performance with the NextSeq 2000 System

Read how the NextSeq 2000 System provides a more comprehensive and streamlined end-to-end workflow with improved variant calling accuracy and performance compared to the AVITI System from Element Biosciences using real-world data.

Download technical note

Expand your access to more data and applications

Epigenetic breakthroughs with the NextSeq 1000/2000 Systems

Learn about innovations of the NextSeq 1000/2000 workflow, including the use of 3D genomics to study the functional context of GWAS variants, in this webinar.

Multiomics

Perform transformative science with access to multiple emerging omics applications.

Compare with other Illumina systems

	MiSeq System	NextSeq 550 System	NextSeq 1000 and NextSeq 2000 Systems	NovaSeq X Series^b
Maximum output per run^a,b	15 Gb	120 Gb	540 Gb^c	8 Tb
Maximum single reads per run^b	25M	400M	1.8B^c	26B
Maximum read length	2 × 300 bp	2 × 150 bp	2 × 300 bp	2 × 150 bp
Informatics options^d	On-premises All DRAGEN Pipelines Cloud DRAGEN Pipelines available on BaseSpace Sequence Hub and Illumina Connected Analytics	On-premises All DRAGEN Pipelines Cloud DRAGEN Pipelines available on BaseSpace Sequence Hub and Illumina Connected Analytics	On-instrument Popular DRAGEN Pipelines available onboard On-premises All DRAGEN Pipelines Cloud DRAGEN Pipelines available on BaseSpace Sequence Hub and Illumina Connected Analytics	On-instrument Popular DRAGEN Pipelines available onboard On-premises All DRAGEN Pipelines Cloud DRAGEN Pipelines available on BaseSpace Sequence Hub and Illumina Connected Analytics

a. Based on Illumina PhiX control library at supported cluster densities.
b. Data is based on single flow cell output. The NovaSeq X Plus System is capable of single flow cell runs or dual flow cell runs. The NovaSeq X System is capable of single flow cell runs.
c. Specifications are based on a P4 flow cell run. P4 flow cells are available for the NextSeq 2000 System only.
d. View key DRAGEN applications for more details.

See all Illumina sequencing platforms

Speak with a specialist

Interested in learning more about the flexibility of NextSeq 1000 and NextSeq 2000 Systems? Contact us today to answer your questions.