Next-generation Sequencing (NGS)

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Next-Generation Sequencing for Beginners

We'll guide you through the basics of NGS, with tutorials and tips for planning your first experiment.

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What is NGS?

Next-generation sequencing (NGS) is a massively parallel sequencing technology that offers ultra-high throughput, scalability, and speed. The technology is used to determine the order of nucleotides in entire genomes or targeted regions of DNA or RNA. NGS has revolutionized the biological sciences, allowing labs to perform a wide variety of applications and study biological systems at a level never before possible.

Today's complex genomics questions demand a depth of information beyond the capacity of traditional DNA sequencing technologies. NGS has filled that gap and become an everyday tool to address these questions.

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Applications of NGS

Next-generation sequencing technology has fundamentally changed the kinds of questions scientists can ask and answer. Innovative sample preparation and data analysis options enable a broad range of applications. For example, NGS allows labs to:

  • Rapidly sequence whole genomes
  • Deeply sequence target regions
  • Utilize RNA sequencing (RNA-Seq) to discover novel RNA variants and splice sites, or quantify mRNAs for gene expression analysis
  • Analyze epigenetic factors such as genome-wide DNA methylation and DNA-protein interactions
  • Sequence cancer samples to study rare somatic variants, tumor subclones, and more
  • Study the human microbiome
  • Identify novel pathogens

Explore Sequencing Methods & Uses

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How Does Illumina NGS Work?

Illumina NGS technology utilizes a fundamentally different approach from the classic Sanger chain-termination method. It leverages sequencing by synthesis (SBS) technology – tracking the addition of labeled nucleotides as the DNA chain is copied – in a massively parallel fashion.

Next-generation sequencing generates masses of DNA sequencing data, and is both less expensive and less time-consuming than traditional Sanger sequencing.2 Illumina sequencing systems can deliver data output ranging from 300 kilobases up to multiple terabases in a single run, depending on instrument type and configuration.

Learn More About SBS Technology

Illumina NGS Methods Guide

In-Depth NGS Introduction

This detailed overview of Illumina sequencing describes the evolution of genomic science, major advances in sequencing technology, key methods, the basics of Illumina sequencing chemistry, and more.

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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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Methods Guide

Key Benefits of NGS

Accessible Whole-Genome Sequencing

Using capillary electrophoresis-based Sanger sequencing, the Human Genome Project took over 10 years and cost nearly $3 billion.

Next-generation sequencing, in contrast, makes large-scale whole-genome sequencing (WGS) accessible and practical for the average researcher. It enables scientists to analyze the entire human genome in a single sequencing experiment, or sequence thousands to tens of thousands of genomes in one year.

Learn More About WGS

Broad Dynamic Range for Expression Profiling

NGS-based RNA-Seq is a powerful method that enables researchers to break through the inefficiency and expense of legacy technologies such as microarrays. Microarray gene expression measurement is limited by noise at the low end and signal saturation at the high end.

In contrast, next-gen sequencing quantifies discrete, digital sequencing read counts, offering a broader dynamic range.1,2,3

Compare Arrays vs. RNA-Seq

Tunable Resolution for Targeted NGS

Targeted sequencing allows you to sequence a subset of genes or specific genomic regions of interest, efficiently and cost-effectively focusing the power of NGS. NGS is highly scalable, allowing you to tune the level of resolution to meet experimental needs. Choose whether to do a shallow scan across multiple samples, or sequence at greater depth with fewer samples to find rare variants in a given region.

Learn more about:

Advances in NGS Technology

Recent Illumina next-generation sequencing technology breakthroughs include:

  • Semiconductor sequencing: The iSeq 100 System combines a complementary metal-oxide semiconductor (CMOS) chip with one-channel SBS to deliver high-accuracy data in a compact system.
  • Patterned flow cell technology: This option offers an exceptional level of throughput for diverse sequencing applications.
  • 75 breakthrough innovations: The NextSeq 1000 and 2000 Systems offer flexibility for emerging applications, a simple workflow, and data analysis in as little as 2 hours.
  • Up to 16 Tb: The NovaSeq X series provides extraordinary sequencing power to fuel data-intensive applications.   
Precision Health

Personalized medicine programs can help match patients to treatments based on their genetic blueprints and improve survival rates, quality of life, and the cost of care.

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How Scientists Use NGS

See how researchers in different fields utilize next-generation sequencing to make breakthrough discoveries.

Genetics of COVID-19 Susceptibility

This UK-wide study uses NGS to compare the genomes of severely and mildly ill COVID-19 patients, to help uncover genetic factors associated with susceptibility.

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Exploring the Tumor Microenvironment

Scientists use single-cell NGS techniques to study cancer microenvironments, elucidate gene expression patterns, and gain insights into drug resistance and metastasis.

Read Article

Cell-Free RNA as a Noninvasive Biomarker

This research highlights the broad potential of circulating cell-free RNA sequencing for biomarker discovery and noninvasive health monitoring.

Read Article


NGS for COVID-19

Next-generation sequencing is uniquely positioned in an infectious disease surveillance and outbreak model. Learn which NGS methods are recommended for detecting and characterizing SARS-CoV-2 and other respiratory pathogens, tracking transmission, studying co-infection, and investigating viral evolution.

Explore Coronavirus NGS Methods
COVID-19 Solutions

Start Using NGS

System Buying Guidance

The resources below offer valuable guidance to scientists who are considering purchasing a next-generation sequencing system.

NGS Experimental Considerations

Learn about read length, coverage, quality scores, and other experimental considerations to help you plan your sequencing run.

Use our interactive tools to help you create a custom NGS protocol or select the right products and methods for your project.

Start Planning Experiments

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Resources for High-Throughput NGS Labs

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Reliable benchtop sequencing solutions

Find out how Illumina commits to upholding a proven track record of benchtop sequencing solutions that empower scientists to advance and accelerate their research.

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Flexible Solutions Using NextSeq 1000 and 2000

Watch a recorded discussion on how the NextSeq 1000/2000 sequencers offer the flexibility and scalability to handle diverse applications and methods for efficient discoveries.

Redefining NGS in Cancer Research

Experts provide an overview of achievements and challenges of NGS in advancing cancer research, including a discussion on how an integrated multiomics approach can be used in future cancer diagnosis and treatment.

Unlocking the Power of Genomics for Surveillance of SARS-CoV-2 Variants

Learn about methods for SARS-CoV-2 surveillance, including requirements, workflow, and analysis.

Genomics News

Podcast stories explore unusual and surprising applications of genomics
Podcast stories explore unusual and surprising applications of genomics

Illumina partners with Naked Genetics to engage audiences in the world of next-generation sequencing

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Efficient cloud data analysis for COPD multiomics project
Efficient cloud data analysis for COPD multiomics project

Researchers at Okayama University in Japan use Illumina Connected Analytics with DRAGEN pipelines for analyzing whole-genome, exome, transcriptome, and metagenome data

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Australia’s latest research investment in improving generational health
Australia’s latest research investment in improving generational health

A milestone study in Melbourne hopes to pave the way to sequencing every child at birth

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Related Solutions

NGS Library Preparation

Fast, simple NGS library prep and enrichment workflows from Illumina to prepare your samples for sequencing.

Sequencing Services

Access fast, reliable next-generation sequencing services that provide high-quality data and offer extensive scientific expertise.

Illumina NGS & Microarray Training

Work with expert Illumina instructors and get hands-on training. We also offer online courses, webinars, videos, and podcasts.