NovaSeq 6000 Sequencing System

Scalable throughput for dynamic study sizes

So many ways to sequence. Scale up and down with a tunable output of up to 6 Tb and 20B single reads in < 2 days.

Broad, deep sequencing for bigger discoveries

Go where discoveries are made. Accelerate your science with immense sequencing breadth and depth when you need it. All on one instrument.

Tunable output for mix and match options

Do what you want. Mix and match flow cell types, and run one or two flow cells at a time. Choose between multiple read lengths, workflows, and more.

Advanced applications. Impactful discoveries.

The NovaSeq 6000 system offers deep and broad coverage through advanced applications for a comprehensive view of the genome. Unlock a full spectrum of genetic variation and biological function with high-throughput sequencing.

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NovaSeq performs whole-genome sequencing more efficiently and cost-effectively than ever. Its scalable output generates up to 6 Tb and 20 billion reads in dual flow cell mode with simple streamlined automated workflows. Configure the system to sequence a trio in one day or up to 48 genomes in ~2 days for the most comprehensive coverage.

Prep
three to five hours
Illumina DNA PCR-Free Prep

A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing or tumor-normal sequencing.

llumina DNA Prep

A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.

Sequence
less than or equal to 44 hours
NovaSeq Reagent Kits v1.5

New kits feature updated reagent formulations with 2x longer shelf life and improved sequencing costs to help power your most impactful studies.

Analyze
less than 25 minutes

*Time per sample, assuming 30x coverage/sample

DRAGEN Germline Pipeline (on BSSH or on DRAGEN server)

The DRAGEN Germline Pipeline v3 aligns and optionally variant calls FASTQ files, outputting a BAM, VCF, or both.

DRAGEN Somatic Pipeline (on BSSH or on DRAGEN server)

The DRAGEN Somatic Pipeline aligns and variant calls Tumor-only or Tumor/Normal FASTQ files, outputting BAM(s) and a VCF.

Representing less than 2% of the genome, WES is a cost-effective alternative to WGS. The NovaSeq 6000 System offers sequencing of up to 500 exomes in a single run using a dual S4 flow cell.

Prep
six hours

*2.5 days total prep time, 6 hours hands-on time

Illumina DNA Prep with Enrichment

This kit uses a fast, user-friendly workflow. On-bead tagmentation chemistry is combined with a simplified, single hybridization protocol to reduce total workflow time.

Sequence
about twenty-five hours
NovaSeq Reagent Kits v1.5

New kits feature updated reagent formulations with 2x longer shelf life and improved sequencing costs to help power your most impactful studies.

Analyze
less than eight minutes

*Time per sample, assuming 100x coverage/sample

DRAGEN Enrichment

This app aligns and optionally variant calls FASTQ, BAM or CRAM files, outputting a BAM, VCF, or both.

Detect coding and multiple forms of noncoding RNA in normal or low-quality samples. With the NovaSeq 6000 System, you can sequence up to 400 transcriptomes in a single run using a dual S4 flow cell.

Prep
about seven hours
Illumina Stranded Total RNA Prep

Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with unparalleled study flexibility.

Sequence
about twenty-five hours
NovaSeq Reagent Kits v1.5

New kits feature updated reagent formulations with 2x longer shelf life and improved sequencing costs to help power your most impactful studies.

Analyze
less than fifteen minutes

*Time per sample, assuming 200x coverage/sample

DRAGEN RNA Pipeline

Performs alignment, quantification, and fusion detection.

Tried-and-true performance

System specifications

Output range
80 - 6000 Gb

Paired end reads per run
1.6B - 40B

Max read length
2 × 250 bp

Run time
13 - 44 hours

View All NovaSeq 6000 Specifications

Compare with NovaSeq X Series & NovaSeq 6000

  NovaSeq 6000 System NovaSeq X Series
Key Features:
  • Scalable throughput
  • Flexible configurations for broad, deep sequencing
  • Streamlined operations and automated flow cell loading
  • Automation-friendly
  • Powered by XLEAP-SBS chemistry, our fastest, highest quality, and most robust SBS chemistry
  • Integrated onboard or cloud-based DRAGEN analysis
  • Groundbreaking sustainability innovations
Run Time: ~13 hr - ~44 hr ~13 hr - ~48 hr
Maximum Output: 6 Tb 16 Tb (for NovaSeq X Plus system)
Maximum Reads per Run: 20 billion single-end reads; 40 billion paired-end reads 52 billion single-end reads; 104 billion paired-end reads (for NovaSeq X Plus system)
Maximum Read Length: 2 x 250 bp 2 x 150 bp
Key Applications: Whole-genome sequencing
Whole-exome sequencing
Whole-transcriptome sequencing
Whole-genome sequencing
Whole-exome sequencing
Whole-transcriptome sequencing
DRAGEN Data Analysis Offerings: (on-premise or cloud)
DRAGEN Germline
DRAGEN Enrichment
DRAGEN Somatic
DRAGEN RNA
(onboard)
DRAGEN Germline
DRAGEN Enrichment
DRAGEN RNA
Featured Products: NovaSeq 6000 Reagent Kits
NovaSeq XP Workflow
Illumina RNA Prep with Enrichment
Illumina DNA PCR-Free Prep
Novaseq X Series Reagent Kits
Illumina DNA PCR-Free Prep
Illumina DNA Prep with Enrichment
Illumina Stranded Total RNA Prep
     

Compare All Illumina Sequencers

Expand Your Access to More Data and Applications

High-Throughput Sequencing

Probe deeper into a single sample for insights or process more samples to improve statistical signficance.

Multiomics

Perform transformative science with access to multiple emerging high-throughput omics applications.

Support for your science

Products & Services
NovaSeq 6000 v1.5 Reagent Kits

New kits feature updated reagent formulations with 2x longer shelf life and improved sequencing costs to help power your most impactful studies.

NovaSeq 6000 Xp Workflow

The NovaSeq 6000 Xp workflow enables labs to load libraries directly into each lane of a NovaSeq 6000 system flow cell, without additional instrumentation.

Illumina RNA Prep with Enrichment

Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.

Illumina DNA PCR-Free Prep

A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.

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Customer Stories

Go behind the science

See what’s possible with the proven NovaSeq 6000 system and NGS technology

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Rady Children’s Institute for Genomic Medicine is using the DNA PCR-Free Prep kit for NovaSeq 6000 to make a potentially record-breaking time-to-diagnosis for children with rare genetic disorders

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Cole Trapnell, PhD is transforming the world of biology by making bioinformatics tools available to all

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OmniSeq, Inc. scaled up to process a large number of both tissue and blood plasma samples every week, batching from 16 to 192 samples in a single run on the NovaSeq 6000

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Genomics England’s human genome initiative (GenOMICC) has launched a study aimed at uncovering genetic factors in susceptibility to COVID-19

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The DRAGEN platform enables GeneDx to scale to whole-genome analysis and identify variants with precision

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