A broad range of applications—all on one platform

Flexibility for virtually any genome, sequencing method, and scale of project

NovaSeq Applications & Methods

Whole-genome sequencing (WGS) is the most comprehensive method for analyzing the genome. Rapidly dropping sequencing costs and the ability to produce large volumes of data make WGS a powerful tool for genomics research of any species, including human, livestock, plants, and disease-related microbes. With the NovaSeq System, you can sequence a tumor-normal trio using a single S1* flow cell or up to 48 genomes per run using dual flow cells.

Whole-exome sequencing (WES) can efficiently identify coding variants across a wide range of applications, including population genetics, genetic disease, and cancer studies.

Representing less than 2% of the genome, WES is a cost-effective alternative to WGS. With the NovaSeq System, you can sequence up to 16 exomes in a single lane using an S1* flow cell or up to 132 exomes using dual S2 flow cells.**

Total RNA sequencing (RNA-Seq) allows researchers to detect both known and novel features in a single assay. This method enables the detection of transcript isoforms, gene fusions, single nucleotide variants, allele-specific gene expression and other features without the limitation of prior knowledge.

Detect coding and multiple forms of noncoding RNA in normal or low-quality samples. With the NovaSeq System, you can sequence up to 16 transcriptomes on a single lane of an S1* flow cell or up to 132 transcriptomes using dual S2 flow cells.

* NovaSeq S1 Reagent Kits are not currently available.
** Sequence from ~20 exomes on a single lane on S1 up to 172 exomes on a dual S2 run.

Introduction to the NovaSeq 6000 System Workflow

Join Brian Steffy, Senior Lab Manager and David Miller, Manager of Sequencing Systems to learn about the streamlined workflow of the NovaSeq System. See first hand why this system is truly our most advanced high-throughput sequencer.

View Video
Introduction to the NovaSeq Series Workflow
Coding Transcriptome Analysis

Detect both known and novel features of the coding transcriptome using sequence-specific capture of RNA coding regions.

Learn More
Targeted DNA Sequencing

Targeted resequencing focuses time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest.

Learn More
Methylation Sequencing

Enhance epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.

Learn More
Gene Expression Profiling with mRNA-Seq

mRNA sequencing (mRNA-Seq) detects known and novel transcripts and measures transcript abundance for accurate, comprehensive expression profiling.

Learn More
De Novo Sequencing

De novo sequencing refers to sequencing a novel genome with no reference sequence available. NGS enables fast, accurate characterization of any species.

Learn More
DNA-Protein Interaction Analysis with ChIP-Seq

Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.

Learn More
Population Studies

Robust, secure, and scalable platforms to aggregate and interpret large-scale genomic data for population sequencing applications.

Learn More
Metagenomics

Comprehensively sample genes in organisms present in a complex sample to evaluate bacterial diversity and detect unculturable microorganisms.

Learn More
Single-Cell RNA Sequencing Kit

View sample data for the Illumina Bio-Rad® SureCell™ Whole-Transcriptome Analysis Kit, designed for single-cell sequencing.

View Data
Illumina Methods Guide

Illumina Methods Guide

Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

Access Guide