NextSeq 550Dx Instrument

The next level in diagnostic power

Benchtop IVD sequencing to enable labs to run diagnostic assays and develop a range of applications from targeted panels to WGS

Scientist starting sequencing run on NextSeq 550Dx Instrument

Run IVD assays and LDT on one instrument

Work within a regulated sequencing workflow to conduct diagnostic tests while retaining the flexibility to develop your own laboratory developed test (LDT). With two operating modes, the NextSeq 550Dx Instrument enables labs to harness Illumina sequencing and array scanning methods to support a wide range of applications.

Improve patient treatment with reliable data and quick TAT

A simple three-step workflow, fast turnaround times (TAT), and integrated analysis software deliver accurate results for time-sensitive clinical IVD testing.

Scientist holding NextSeq 550Dx sequencing reagent

Ensure the highest standards in clinical diagnostics

The NextSeq 550Dx Instrument and sequencing reagents are:

In compliance with global regulatory standards including FDA and IVDR regulations
Developed under design control principles
Manufactured under Current Good Manufacturing Practices (cGMPs)
21 CFR part 11 compliant software
Verified for consistent assay performance

Illumina DNA Prep Enrichment Dx library preparation kit

Design custom NGS IVD assays

The NextSeq 550Dx Instrument is part of a robust IVD development toolkit when paired with the Illumina DNA Prep Enrichment Dx library preparation kit and the NextSeq 550Dx Reagent Kit. Develop your own assays with regulated components or benefit from a growing set of Illumina clinical assays.

Contact an Illumina representative for more information about IVD development partnerships.

Learn more about NGS for IVD assay development

The reliability and quality of a clinical instrument

Instrument specifications

Output range
≥ 90 Gb
Paired-end reads per run
≥ 300M
Max read length
2 × 150 bp
Run time
< 35 hr

View all NextSeq 550Dx Instrument specifications

Simplified three-step workflow

The NextSeq 550Dx Instrument is easily configured, scalable, and user-friendly.

Prepare libraries

Benefit from a pipeline of IVD tests in development or design your own. Generate indexed libraries and create runs in Local Run Manager.

Sequence

Add library to the ready-to-use NextSeq 550Dx reagent cartridge, load, and start run. Generate data < 35 hours.

Analyze data

Automatically launch data analysis with Local Run Manager and get results in a few hours. Leverage BaseSpace apps for additional analysis options.

Diagnostic and clinical research applications

Run IVD assays using targeted panels and a wide range of clinical research applications, including exome sequencing, targeted gene sequencing, whole-transcriptome sequencing, and cytogenomic arrays.

View all NextSeq 550Dx Instrument applications

Featured applications

Molecular diagnostics

Apply advances in genetic analysis to fill crucial needs in disease detection, prenatal and reproductive care, and precision medicine.

IVD assay development

Gain access to a robust IVD pipeline in partnership with Illumina and design custom NGS assays for your clinical lab.

Compare with MiSeqDx and NovaSeq 6000Dx Instruments (in Diagnostic Mode)

	NextSeq 550Dx Instrument^a	MiSeqDx Instrument^a	NovaSeq 6000Dx Instrument^b,c
Run time	< 35 hr	24 hr	≤ 45 hr
Maximum output per run	≥ 90 Gb	≥ 5 Gb	≥ 3 Tb
Maximum paired-end reads per run	> 300M	≥ 15M	≥ 20B
Read length	2 × 150 bp	2 × 150 bp^d	2 × 150 bp
Data quality	> 75% of bases higher than Q30	≥ 80% of bases higher than Q30	≥ 85% of bases higher than Q30
Data analysis offerings^e	Dx Mode: Local Run Manager, dedicated DRAGEN server RUO Mode: Local Run Manager, Illumina Connected Analytics, on-premises DRAGEN server	Dx Mode: Local Run Manager RUO Mode: Local Run Manager, Illumina Connected Analytics, on-premises DRAGEN server	Dx Mode: Dedicated DRAGEN server RUO Mode: Dedicated DRAGEN server, BaseSpace Sequence Hub, Illumina Connected Analytics

a. Libraries generated with TruSeq Custom Amplicon Kit Dx.

b. Libraries generated with Illumina DNA Prep with Enrichment Dx.

c. Based on a single S4 flow cell.

d. Maximum read length for the MiSeqDx Instrument is 2 x 300 bp, depending on the assay used.

e. A dedicated DRAGEN server is paired with an Illumina sequencing system and can be used to plan secondary analysis as part of sequencing run using the Illumina Run Manager. An on-premises DRAGEN server does not communicate directly with the sequencing system but can ingest and process data from any Illumina sequencing system via a command-line.

See all Illumina sequencing platforms

Intended Use for the NextSeq 550Dx Instrument

United States:

The NextSeq 550Dx Instrument is intended for targeted sequencing of DNA libraries from human genomic DNA extracted from peripheral whole blood or formalin-fixed, paraffin-embedded (FFPE) tissue when used with in vitro (IVD) diagnostic assays. The NextSeq 550Dx Instrument is not intended for whole genome or de novo sequencing. The NextSeq 550Dx Instrument is to be used with specific registered, certified, or approved in vitro diagnostic reagents and analytical software.

European Union:

The NextSeq 550Dx instrument is intended for sequencing of DNA libraries when used with in vitro diagnostic assays. The NextSeq 550Dx instrument is to be used with specific registered, certified, or approved in vitro diagnostic reagents and analytical software.