Instruments

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

1
Library prep

Illumina DNA PCR-Free Prep

High-performing, fast, and integrated PCR-free workflow for sensitive applications such as human whole-genome sequencing or tumor–normal sequencing.

Illumina DNA Prep

Fast, integrated workflow for a wide range of applications, including sequencing of whole human genomes, amplicons, plasmids, and microbial genomes.

2
Sequence

NovaSeq 6000 Reagent Kits v1.5

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for reliable, high-throughput sequencing on the NovaSeq 6000 System. Multiple sequencing output and read length options available.

3
Analyze

DRAGEN Germline app (on BaseSpace Sequence Hub or DRAGEN server)

Aligns and calls variants from FASTQ files, outputting BAM and VCF files.

DRAGEN Somatic Pipeline app (on BaseSpace Sequence Hub or DRAGEN server)

Aligns and calls tumor-only or tumor–normal variants from FASTQ files, outputting BAM and VCF files.

Find WGS education

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

1
Library prep

Illumina DNA Prep with Enrichment

Fast, integrated DNA-based library preparation and enrichment combining on-bead tagmentation with a single hybridization protocol for targeted sequencing applications.

2
Sequence

NovaSeq 6000 Reagent Kits v1.5

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for reliable, high-throughput sequencing on the NovaSeq 6000 System. Multiple sequencing output and read length options available.

3
Analyze

DRAGEN Enrichment app

Aligns and calls variants from FASTQ, BAM, or CRAM files, outputting BAM and VCF files.

Find exome sequencing education

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.

1
Library prep

Illumina Stranded Total RNA Prep with Ribo-Zero Plus or Ribo-Zero Plus Microbiome

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

2
Sequence

NovaSeq 6000 Reagent Kits v1.5

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for reliable, high-throughput sequencing on the NovaSeq 6000 System. Multiple sequencing output and read length options available.

3
Analyze

DRAGEN RNA Pipeline app

Next-generation sequencing secondary analysis of RNA transcripts, including alignment, quantification, and fusion detection.

Find whole-transcriptome sequencing education

Resource spotlight

Introduction to the NovaSeq 6000 System workflow

Learn about the streamlined workflow of the NovaSeq 6000 System. See firsthand why this system is an advanced high-throughput sequencing system.

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.

mRNA sequencing

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

Population genomics

Aggregate and interpret large-scale genomic data for population studies 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.

Single-cell RNA sequencing

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

De novo sequencing

Enable fast, accurate characterization of novel genomes in cases where no reference sequence is available for alignment.

Metagenomics

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

Proteomics

Combining proteomics assays with the power and scalability of NGS enables simultaneous interrogation of thousands of proteins in a single sample.

Targeted sequencing

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

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