NextSeq 550 Sequencing System

Fuel your lab

Combine proven NGS technology with tunable output to enable sequencing and array capabilities across a range of applications 


Discover the NextSeq 550 System

Learn how the NextSeq 550 System is enhancing research in reproductive and genetic health and why it’s being rapidly adopted in small and large genetic testing labs. Get a glimpse into the advantages of this integrated, cost-effective solution for diverse applications.

Keep pace with genomics

Harness the complementary powers of sequencing and genotyping on a single instrument. Facilitate discoveries in small and large labs with:

  • One-day turnaround for many popular sequencing applications
  • Configurable output based on sample volume and coverage needs
  • A single DNA-to-results workflow
Scale with confidence

Support evolving needs with a robust, efficient, and rapid workflow that enables tunable output:

  • Shift from high- to low-throughput sequencing with two flow cell configurations
  • Sequence a broad range of samples per run
  • Benefit from the full suite of Illumina library preparation and target enrichment solutions
Perform world-class bioinformatics

Access fast and accurate data analysis pipelines through Illumina DRAGEN secondary analysis on BaseSpace Sequence Hub. Cloud-based, local, or on-premises server options deliver secure and user-friendly genomic insights to fuel your research.

Explore further with microarray scanning

Easily transition between high-throughput sequencing and array scanning, powered by bead-based BeadArray technology and proven Infinium chemistry. By integrating two technologies into a single instrument, the NextSeq 550 System saves instrument costs and limited lab space while maximizing available applications.

Reliable benchtop sequencing

System Specifications

  • Output range
    16.25 - 120 Gb
  • Reads per run
    130 - 400 million
  • Max read length
    2 x 150 bp
  • Run time
    12 -30 hr

One simple, integrated workflow from prep to analysis


Prepare libraries for a range of applications with a large menu of Illumina library prep options.


Generate data in less than one day with automated sequencing.


Leverage DRAGEN secondary analysis via an on-premises server or on BaseSpace Sequence Hub for applications such as exome and transcriptome sequencing.


Share data instantly on BaseSpace Sequence Hub and enable secure, expandable storage.

Dive deeper

From gene expression profiling to small whole-genome sequencing, the NextSeq 550 System provides reliable, accessible insights with integrated sequencing and array scanning capabilities.

Featured applications

Exploring the tumor microenvironment

Learn how researchers at the Garvan Institute of Medical Research in Sydney gain insights into 150 different proteins on the surface of thousands of single cells for investigating cancer microenvironments.

Compare with other NextSeq Systems


NextSeq 550 System

NextSeq 550Dx Instrumentb


NextSeq 1000 and NextSeq 2000 Systems

Maximum output per runa 120 Gb 121 Gb 360 Gb
Maximum reads per run 400 million 400 million 1.2 billiona
Maximum read length 2 x 150 bp 2 x 150 bp 2 x 150 bp
Informatics options

On-Premises Server
All DRAGEN pipelines except metagenomics

Cloud via BSSH
Most DRAGEN pipelines and select options

On-Premises Server
All DRAGEN pipelines except metagenomics

Cloud via BSSH
Most DRAGEN pipelines and select options

On-Premises Server
Illumina DRAGEN secondary analysis

BSSH applications
Illumina Connected Analytics

a. Based on Illumina PhiX control library at supported cluster densities.
b. For In Vitro Diagnostic Use. Not available in all regions and countries.

Popular products

NextSeq 500/550 v2.5 Kits

Reagent v2.5 kits use a resilient flow cell that maintains starting fluorescent intensity, improving stability and performance compared to earlier versions.

Illumina DNA Prep with Enrichment

A complete targeted resequencing solution for a wide range of applications, with fast integrated workflow and options for custom and fixed enrichment panels.

Illumina RNA Prep with Enrichment

A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.

Speak with a specialist

Contact us for more information and learn if the NextSeq 550 System is right for your lab.