The NextSeq 500 Sequencing System has been discontinued. The NextSeq 550 System is an alternative solution that provides the increased flexibility of microarray scanning in addition to sequencing.

NextSeq 550 System

NextSeq Instrument Comparison

  NextSeq 550 System NextSeq 550 Dx System*** NextSeq 1000 & NextSeq 2000 Systems
For Customers who need array scanning and mid-throughput sequencing capacity Customers who need an IVD cleared system with tight change control Customers who want a cost-efficient sequencer that offers scalability for evolving needs and supports emerging applications
Key Features
  • Array scanning
  • Mid and high output kits available
  • IVD including partnerships
  • Array scanning (in Research mode)
  • Mid and high output kits available
  • Diagnostic mode for clinical testing
  • Research mode for clinical research applications
  • Integrated DRAGEN data analysis
  • Best-in-class workflow
  • Trade-in promotions available
Run Time 12–30 hours 12–30 hours 11-48 hours
Maximum Output 120 Gb* 121 Gb* 330 Gb*
Maximum Reads per Run 400 million 400 million 1.1 billion*
Maximum Read Length 2 × 150 bp 2 × 150 bp 2 × 150 bp
Product Highlights The NextSeq 550 System combines tried-and-true instrument technologies and tunable output with sequencing and array capabilities. Offers a validated high-throughput platform with access to an ever-expanding pipeline of clinical applications in the fields of oncology, reproductive health, and more. Cost-efficient flexibility for new and emerging applications, enabling deeper, larger studies on a benchtop platform.
Key Applications
  • Targeted sequencing (amplicon-based, gene panel)
  • Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)
  • Arrays
  • Diagnostic Mode: NGS IVD Applications
  • Research Mode: Same applications as NextSeq 550
  • Single-cell profiling
  • Small whole-genome sequencing
  • Exome and large panel sequencing (enrichment-based)
  • Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)
DRAGEN Data Analysis Offerings

DRAGEN via the cloud through BaseSpace Pipelines (Most DRAGEN pipelines and select options)

DRAGEN on-premise via server (All DRAGEN pipelines excluding metagenomics)

DRAGEN via the cloud through BaseSpace Pipelines (Most DRAGEN pipelines and select options)

DRAGEN on-premise via server (All DRAGEN pipelines excluding metagenomics)

DRAGEN onboard analysis

For customers who may not have bioinformatics expertise to maintain an on-premise server, and who won’t utilize BaseSpace Sequence Hub, we offer DRAGEN as an onboard capability for NextSeq 2000 customers, with access to select DRAGEN informatics pipelines**:

  • DRAGEN Enrichment Pipeline
  • DRAGEN RNA Pipeline
  • Gene fusion detection
  • Single-Cell RNA
Featured Products

Research Mode:

Diagnostic Mode:

  Explore NextSeq 550 Explore NextSeq 550Dx Explore NextSeq 1000 & 2000

* Specifications based on Illumina PhiX control library at supported cluster densities.
** Differential Expression and DNA Amplicon coming in spring of 2021.
*** For In Vitro Diagnostic Use. Not available in all regions and countries.

The Illumina Community

The Illumina Community

Collaborate with other scientists in the Illumina Online Community. Discuss best practices, troubleshoot, and learn about how others are using Illumina sequencers, library preparation kits, and automated data analysis to fuel their research.

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16.25–120 Gb
output range

130–400 million
reads per run

2 x 150 bp
max read length
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