Key Applications and 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 pair or germline trio using a single S1 flow cell or up to 48 genomes per run using dual S4 flow cells.
Prep
3–5 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.
Illumina DNA Prep
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
BaseSpace Clarity LIMS
A laboratory information management system that helps labs track samples and optimize workflows.
Sequence
Up to 44 hours
NovaSeq Reagent Kits
Ready-to-use cartridge-based reagents and multiple flow cell configurations create a highly flexible and streamlined workflow with scalable throughput to meet project needs.
Analyze
<3 hours
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.
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 20 exomes in a single lane using S1 or up to 200 exomes using a dual S2 flow cell run.
Prep
2.5 days/6 hours hands-on
TruSeq DNA Library Prep for Enrichment
A low-cost exome sequencing solution that delivers exceptional target coverage. This workflow is also compatible with unique dual index kits, and the exome panel is available from Integrated DNA Technology (IDT).
BaseSpace Clarity LIMS
A laboratory information management system that helps labs track samples and optimize workflows.
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
~25 hours
NovaSeq Reagent Kits
Ready-to-use cartridge-based reagents and multiple flow cell configurations create a highly flexible and streamlined workflow with scalable throughput to meet project needs.
Analyze
2–3 hours
BaseSpace Enrichment App
Rapid alignment and variant detection for structural and copy number variant calling, variant annotation, and enrichment metrics calculation.
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 8 transcriptomes on a single lane of an SP flow cell or up to 164 transcriptomes in a dual S2 flow cell run.
Prep
~7 hours
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with unparalleled study flexibility.
BaseSpace Clarity LIMS
A laboratory information management system that helps labs track samples and optimize workflows.
Sequence
~25 hours
NovaSeq Reagent Kits
Ready-to-use cartridge-based reagents and multiple flow cell configurations create a highly flexible and streamlined workflow with scalable throughput to meet project needs.
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.
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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.
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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.
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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 InterviewMore 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.
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