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High-Throughput Sequencing

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Bringing greater insights, answers, and breakthroughs to light

See what is possible through the latest advances in Illumina high-throughput sequencing technology

Advantages of High-Intensity Sequencing

The latest innovations in Illumina high-throughput sequencing technology power high-intensity sequencing applications to generate dramatically more data for more impactful insights. Increasingly, scientists are leveraging the advantages of high-intensity sequencing applications with our simplified, cost-efficient high-throughput sequencing workflows.

High Intensity Sequencing - Advantages

Improve Statistical Power

Increased statistical power from larger sample sizes for more impactful conclusions.

Access Previously Missed Information

See the full breadth of variation with whole-genome or whole-transcriptome sequencing.

Get Multidimensional Insights

Multidimensional insights with sequencing provide a single readout from multiple -omes across DNA, RNA, and protein.

Increase Analytical Resolution

Transition to high-resolution approaches, including single-cell sequencing and spatial analyses for insights into complex tissues.

High-ThrougHput Sequencing Technology Innovations

The latest advances in Illumina sequencing have enabled high-intensity sequencing applications, bringing insights that were unimaginable even a few years ago and removing barriers with every technological innovation.

Get an unparalleled breadth of targets. Create multi-dimensional insights with optimized indexing strategies. Illumina high-throughput sequencing provides a single robust readout for multiple -omes.


Amplify your insights. Cast a wider net with larger sample sizes. Cost-effective high-throughput sequencing opens up your options to do high-intensity sequencing applications and gain additional insights for a more comprehensive view of your sample.

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Discover More with Multiomics

Combine genomic data with data from other modalities such as transcriptomics, epigenetics, and proteomics to measure gene expression, gene activation, and protein levels. High-throughput omics profiling studies enable a more comprehensive understanding of molecular changes contributing to normal development, cellular response, and disease.

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Popular High-Throughput Sequencing Methods

Achieve impactful insights and accelerate your lab’s work with these methods.

Bulk Sequencing Methods
  Key Benefit Library Prep System(s) Informatics


Methylation Sequencing Explore the methylome
ChIP-Seq Understand gene regulation
ATAC-Seq Map chromatin accessibility across the genome
  Key Benefit Library Prep System(s) Informatics

Transcriptomics + Proteomics

BEN-Seq Get gene expression and surface protein expression profiles simultaneously
  Key Benefit Library Prep System(s) Informatics

Liquid Biopsy

ctDNA Sequencing Noninvasive approach detecting ctDNA in plasma from solid tumors
  Key Benefit Library Prep System(s) Informatics

Solid Tumor

Targeted Cancer Screening Identify all mutational classes and IO biomarkers in a single assay
Single-Cell Methods
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RNA Single-Cell RNA-Seq Reveal transcriptome cell-to-cell variation Single-Cell RNA-Seq method is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with library prep and data analysis provided by 10X Genomics or through the Illumina DRAGEN Single Cell BaseSpace App. Learn More at 10X
    Key Benefit Solution Learn More
Epigenetics Single-Cell ATAC-Seq Access chomatin accessibility patterns to view cell-to-cell variation Single-Cell ATAC-Seq method is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with library prep and data analysis provided by 10X Genomics and open source tools such as Bowtie 2 and Seurat by the Satija Lab. Learn More at 10X
    Key Benefit Solution Learn More
RNA + Epigenetics Single-Cell Gene Expression + ATAC-Seq Correlate transcriptome and chomatin accessibility patterns at the single-cell level Utilize the Multiome Single-Cell ATAC-Seq + gene expression prep kit from 10X genomic on the NovaSeq 6000 and NextSeq 2000 platforms. Download Tech Note
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RNA + Proteomics CITE-Seq Evaluate gene expression and surface protein expression levels simultaneously at single-cell resolution CITE-Seq is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with compatible antibodies from BD or BioLegend and single-cell prep kits from 10X Genomics. Analysis tools can also be found from 10x Genomics, BD or BioLegend. Learn more about CITE-Seq on BioLegend site
    Key Benefit Solution Learn More
DNA + Protein Proteomics Correlate known tumor genomic variants to cell-surface proteins at single-cell resolution This DNA + protein panel for tumor samples is compatible with the NextSeq 2000 platform with compatible antibodies from BioLegend and the prep Instrument, prep kit and analysis tool kit from Mission Bio Learn more about Mission Bio's tapestri platform that enables proteomics with sequencing
Spatial Methods
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RNA RNA-Seq Spatial Understand the gene expression patterns from a particular region of interest within an FFPE or fresh frozen tissue sections RNA-Seq Spatial sequencing is compatible with NovaSeq 6000 and NextSeq 2000 Platforms, with library prep and data analysis provided by NanoString Download the Tech Note
    Key Benefit Solution Learn More
RNA + Proteomics CITE-Seq Spatial Correlate targeted gene expression and protein expressions patterns from FFPE or fresh frozen tissue sections CITE-Seq Spatial sequencing is compatible with NovaSeq 6000 and NextSeq 2000 Platforms, with library prep and data analysis provided by NanoString Learn more about spatial profiling for protein assays at Nanostring

High-Throughput Sequencers

Deeper Discoveries with the NovaSeq 6000 System

By far our most powerful instrument, now with improved economics and an output of up to 6 Tb and 20 B reads in < 2 days. Unlock the full spectrum of genetic variation and biological function with high-throughput sequencing on the NovaSeq 6000. Advances in reagents support a vast breadth of targets and complex indexing strategies at an accessible price point.

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High-Throughput Sequencers

"We basically cut the price of single-cell sequencing in half just by getting this machine, and that's huge."

Accessibility for New and Emerging Applications with the NextSeq 2000 System

NextSeq 2000 System is redesigned from the ground up to maximize future proofing, offering sequencing power for high-throughput applications. With adjustible output and scalability for evolving needs and larger studies, the system and reagents make a vast variety of data-rich multiomics applications accessible, including whole-exome, and single-cell sequencing.

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High-Throughput NGS Data Analysis

Perform Ultra-Rapid, User-Friendly Data Analysis

DRAGEN Bio-IT Platform

The platform for ultra-rapid secondary genomic analysis with highly accurate results, diverse applications, and frequent updates. DRAGEN can process NGS data for an entire human genome at 30x coverage in about 25 minutes.

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Aggregate, Explore, and Share Large Volumes of Data

Illumina Connected Analytics

This comprehensive cloud-based data management and analysis software platform empowers researchers to manage, analyze, and interpret large volumes of multiomics data in a secure, scalable, and flexible environment. The platform is built for high-volume operations limited by data silos and a lack of bioinformatics and data science tools.

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Automate Your Library Prep

These walk-away automation methods for Illumina kits eliminate the need to develop your own method and can help you reduce hands-on time and minimize errors.

Access More Data for More Insights

Find information and resources to help simplify the process of setting up an informatics infrastructure and data analysis pipeline for high-intensity sequencing projects.

Multiplex Sequencing

Pool and sequence large numbers of NGS libraries simultaneously during a single run.

High-Throughput Sequencing Supports Genome Center Growth

The Deakin Genomics Centre uses a NovaSeq 6000 System for highthroughput, large-scale sequencing projects that lower sequencing costs and provide a faster turnaround of sequencing data to their scientists.

Identify Breast Cancer Targets with High-Throughput NGS

Garvan Institute scientists are sequencing more than a million breast cancer cells to help create a comprehensive cellular atlas of breast cancer.

Featured Webinars

Deploy High-Throughput Proteomics with NGS

Learn how to take multiplex proteomics to the next level and discover protein biomarkers using Illumina sequencers.

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Omics-Based Precision Medicine Methods

Whole-genome sequencing is an increasingly viable approach for precision diagnosis in clinical care.

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Related Content

Trade In Your HiSeq System

Interested in trading in your HiSeq System for the latest high-throughput sequencer with more discovery power? You may be eligible to trade in your existing instrument for a new NovaSeq 6000 System.

Illumina Online Community

Connect with others using the same methods, see tips on experimental planning and troubleshooting, and find answers to common questions.

Everything You Need at a Glance

Explore Illumina high-throughput sequencing options. Get additional training, find software, plan experiments, purchase, and get support.