Sequencing
Sequencing Microarrays Popular Applications Multiomics

Sequencing

Understanding genetic sequencing methods and applications

What is genetic sequencing?

Sequencing is used to determine the order of nucleotides in small targeted genomic regions or entire genomes. Illumina sequencing enables a wide variety of applications, allowing researchers to ask virtually any question related to the genome, transcriptome, epigenome, and proteome of any organism. Next-generation sequencing (NGS) methods differ primarily by how the DNA or RNA samples are prepared and the data analysis options used.1

Key sequencing methods

DNA sequencing

Analyze the entire genome, focus on regions of interest with whole–exome and targeted sequencing, or study DNA-protein interactions.

RNA sequencing

Take advantage of a broad range of techniques, from targeted RNA to single-cell and whole-transcriptome sequencing.

Methylation sequencing

Explore how both genome-wide analysis and targeted approaches can provide insight into methylation patterns at a single nucleotide level.

Long-read sequencing

Discover how long-read sequencing enables the sequencing of much longer DNA fragments than traditional short-read sequencing methods.

Sequencing system portfolio

View sequencing systems, compare features, and learn how to choose the right platform for your needs.

Explore platforms
Close up image of a female scientist pipetting clear liquid into tube; NextSeq 1000/2000 reagent cartridge and box in the background.

Library preparation

Find out more about how library prep works and explore user-friendly solutions. Options are available for a broad range of sequencing methods, including whole-genome sequencing, whole-exome and targeted sequencing, RNA sequencing, methylation sequencing, and more.

Common sequencing applications

Cancer research

NGS-based sequencing methods allow cancer researchers to detect rare somatic variants, tumor subclones, and circulating DNA fragments.

Explore cancer sequencing methods

Microbiology research

From environmental metagenomics studies to infectious disease surveillance and more, sequencing can help researchers gain genetic insight into bacteria and viruses.

Learn more about microbial genomics

Complex disease research

Illumina sequencing is introducing new avenues for understanding autoimmune and rheumatic diseases, atherosclerosis, neurological diseases, and psychiatric disorders on a molecular level. 

Learn more about complex disease genomics

Reproductive health

Advance research in reproductive health with comprehensive sequencing insights.

Explore reproductive health solutions

Beginner's guide to next-generation sequencing

Considering bringing next-generation sequencing to your lab but unsure where to start? These resources cover key topics in NGS and are designed to help you plan your first experiment.

Get started

Sequencing FAQ

Sequencing is the determination of the precise order of each base within a DNA or RNA molecule. Sequencing methods and turnaround times vary widely depending on the application or research study. Next-generation sequencing, due to its high resolution and large data output, is considered the standard for exploratory research.

Genotyping, by contrast, is a more targeted approach that is used to gain genetic insights at predetermined genomic regions or loci. As such, genotyping is often preferred by researchers for studies requiring a faster turnaround, including high-throughput analyses confirming the presence of known genetic variants.2

Watch the Illumina sequencing webinar to learn how academic core labs are adopting advancements on the Illumina NovaSeq X Series for faster and higher-quality sequencing services. 

Watch the DNA sequencing technology webinar to discover DNA sequencing tools and how these platform innovations are enabling genotyping at a lower cost and at a greater scale for animal breeding research.

The standard steps in a next-generation sequencing workflow, regardless of the specific technology, consist of the following: extraction and sample preparation, library preparation (including quality control), sequencing, bioinformatics analysis, and interpretation.

Learn about NGS workflow steps in greater detail and explore additional sequencing resources.

Discover recent Illumina sequencing innovations in this on-demand webinar from Jacob Thaysen, CEO, Illumina at Advances in Genome Biology and Technology (AGBT) 2026.

Sequencing methods and technologies have evolved through generational advancements, with each generation offering scientists the ability to solve different research challenges.

  1. First-generation sequencing (Sanger Sequencing): This foundational technology is considered the gold standard and used for accurate but low-throughput interrogation of a small region of DNA on a limited number of samples or genomic targets.
  2. Next-generation sequencing (NGS)/short-read sequencing: NGS is characterized by short-read sequencing systems that use parallel processing to simultaneously sequence millions to billions of DNA fragments. This advancement significantly increased throughput while reducing costs and turnaround time, making whole-genome sequencing (WGS) and transcriptomics more broadly accessible. Furthermore, technological innovations have expanded its capabilities to successfully map challenging and highly repetitive regions.3
  3. Long-read sequencing: This technology is designed to enable the generation of continuous single-molecule reads. With a more contiguous view of the genome, this method provides researchers the resolution to map challenging or repetitive genetic regions.

Explore the Illumina innovation roadmap to learn about NGS technologies and products to empower researchers to perform studies at the throughput, scale, and price that meets their research objectives.

Discover how proximity mapped read technology maintains the link between the original long DNA template and short sequencing reads to enable the resolution of difficult-to-map regions of the genome.   

In the context of NGS, depth of coverage describes the average number of sequencing reads covering a specific base in the genome. It is expressed as fold coverage and often considered alongside breadth of coverage.

Coverage depth helps determine confidence in variant detection, variant calling, and other downstream analyses. Specific sequencing coverage requirements vary by application and method (eg 30× to 50× for human WGS).4

Explore coverage depth recommendations to learn how to estimate the depth of coverage that is required for your research. 

Several planning phases should be considered to get started with an NGS project. These phases generally include:

  1. Defining the research objective 
  2. Selecting an appropriate library prep kit 
  3. Determining the required throughput and sequencing system to match data and budget requirements
  4. Planning downstream data analysis needs

Illumina offers numerous educational and technical resources to help researchers get started with sequencing. Learn next-generation sequencing works and discover a broad range of experiments that you can perform with NGS.

Visit our NGS for beginners page for a variety of educational videos and resources to get you started.

/ Results

New to NGS eBook

With this comprehensive, easy-to-follow guide you’ll learn about NGS methods, workflows, data analysis solutions, and more for bringing NGS into your lab.

Additional resources

Introduction to NGS

NGS has revolutionized the biological sciences. Learn how it compares to alternative methods, and find out how Illumina technology works.

NGS vs Sanger sequencing

Understand the key differences and when next-generation sequencing can be a more effective option than Sanger sequencing.

Illumina resources and tools

Educational and scientific tools to help identify the best approach, manage your workflow, purchase what you need, and get support.

Sequencing data analysis

Find intuitive data analysis solutions that allow you to spend more time doing research and less time setting up workflows.

Sequencing training

Get hands-on sequencing training from expert instructors. We offer live or self-paced online courses and other educational resources.

Speak to a specialist

Talk to an expert to learn more about sequencing solutions.

References

  1. Grassi L, Harris C, Zhu J, Hatton D, Dunn S. Next-generation sequencing: A powerful multi-purpose tool in cell line development for biologics production. Comput Struct Biotechnol J. 2025;27:1511-1517. Published 2025 Apr 3. doi:10.1016/j.csbj.2025.04.006 
  2. Yang Y, Del Gaudio D, Santani A, Scott SA. Applications of genome sequencing as a single platform for clinical constitutional genetic testing. Genet Med Open. 2024;2:101840. Published 2024 Mar 20. doi:10.1016/j.gimo.2024.101840 
  3. Ahsan MU, Liu Q, Perdomo JE, Fang L, Wang K. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nat Methods. 2023;20(8):1143-1158. doi:10.1038/s41592-023-01932-w 
  4. Bhérer C, Eveleigh R, Trajanoska K, et al. A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome. NPJ Genom Med. 2024;9(1):8. Published 2024 Feb 7. doi:10.1038/s41525-024-00390-3