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NovaSeq Applications & Methods

A broad range of applications—all on one platform

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

Key Applications and Methods

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 200x 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 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 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.

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

Featured NovaSeq Stories

New Liquid Biopsy and High-Throughput Assays Join TruSight Oncology Portfolio

The first liquid biopsy solution for detecting cancer biomarkers on the NovaSeq 6000 System is the latest addition to our portfolio of comprehensive cancer profiling assays.

Read Article
The Time is Now for Microbiome Studies

Dissecting host—microbial relationships with the NovaSeq 6000 System gives researchers and pharmaceutical companies data to refine drug discovery.

Read Interview
Uncovering the Intracellular Communication of Tumors

Using the NovaSeq 6000 System, scientists are looking at the microenvironment surrounding tumors. Understanding this environment could tell us more about how cancer cells migrate and become drug resistant.

Read Interview

More Applications and Methods

Target Enrichment

Use sequence-specific hybridization to analyze genomic regions of interest.

Coding Transcriptome Analysis

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

Targeted DNA Sequencing

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

Methylation Sequencing

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

Gene Expression Profiling with mRNA-Seq

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

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.

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.

Population Studies

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

Metagenomics

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

Single-Cell RNA Sequencing

Assess the individual contributions of single cells in complex tissues by profiling the transcriptome.

ctDNA Sequencing

NGS offers the sensitivity and specificity that cancer researchers need to detect low levels of ctDNA in the bloodstream.

RNA Drug Response Biomarker Discovery

Find out how to utilize RNA-Seq to discover and profile RNA-based drug response biomarkers. Access resources designed to help new users adopt this application.

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

Related Solutions

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Microbial Genomics

Next-generation sequencing (NGS) is changing microbial genomics. Use NGS to discover novel microbes, monitor outbreaks, analyze food sources, and more.

Complex and Genetic Disease Research

Comprehensive array and next-generation sequencing solutions to accelerate research of various genetic complex diseases.