NovaSeq 6000 Sequencing System applications and methods

Unlock the possibilities

Scalable, flexible sequencing across a range of sample types, methods, and applications 

NovaSeq 6000 flow cell

Key applications and methods

NovaSeq 6000 System performs whole-genome sequencing (WGS) efficiently and cost-effectively. Its tunable output generates up to 6 Tb and 20B reads in dual flow cell mode with streamlined workflows. Configure the system to sequence a trio in one day or up to 48 genomes in ~2 days for comprehensive coverage.

Read WGS application note

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Library prep
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Sequence
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Analyze

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

Read customer interview: rare disease studies

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Library prep
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Sequence
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Analyze

Detect coding and multiple forms of noncoding RNA in normal or low-quality samples. The NovaSeq 6000 System offers sequencing of up to 400 transcriptomes in a single run using a dual S4 flow cell.

Read single-cell RNA application note

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Library prep
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Sequence
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Analyze

More applications and methods

ChIP-Seq

Analyze protein interactions with DNA for genome-wide surveys of gene regulation.

Methylation sequencing

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

Coding transcriptome analysis

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

Population studies

Aggregate and interpret large-scale genomic data for population sequencing applications in a robust, secure, and scalable platform.

ctDNA sequencing

Use next-generation sequencing for sensitive and specific detection of low levels of circulating tumor DNA (ctDNA) in the bloodstream.

RNA drug response biomarker discovery

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

De novo sequencing

Enable fast, accurate characterization of novel genomes with no reference sequence available for any species.

Single-cell RNA sequencing

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

Gene expression profiling with mRNA-Seq

Detect known and novel transcripts and measure transcript abundance for accurate, comprehensive expression profiling.

Targeted DNA sequencing

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

Metagenomics

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

Target enrichment

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

How others use this instrument

See what’s possible with the NovaSeq 6000 System

New PCR-free prep expedites whole-genome sequencing

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