DNA Sequencing
DNA Sequencing RNA Sequencing Methylation Sequencing Library Preparation High-Throughput Sequencing

DNA sequencing

NGS technology enables massively parallel DNA sequencing for a deeper understanding of the genetic code

DNA sequencing on NextSeq 1000 / NextSeq 2000

Introduction to DNA sequencing

DNA sequencing is a highly scalable approach that can be applied to genes, DNA regions of interest, or the entire genome, enabling researchers to investigate and better understand health and disease. Next-generation sequencing (NGS) technology can be used to sequence DNA from virtually any organism, providing valuable information in response to almost any biological question.

Illumina NGS technology uses clonal amplification and sequencing by synthesis (SBS) chemistry to enable rapid, accurate DNA sequencing. The process simultaneously identifies DNA bases while incorporating them into a nucleic acid chain. Each base emits a unique fluorescent signal as it is added to the growing strand, which is used to determine the order of the DNA sequence.

Benefits of DNA sequencing with NGS

Discover the advantages of DNA sequencing to better understand human health and disease

High throughput and speed

Sequences large stretches of DNA in a massively parallel fashion, offering advantages in throughput and scale compared to capillary electrophoresis–based Sanger sequencing

High-resolution insights

Provides high resolution to obtain a base-by-base view of a gene, exome, or genome

Accurate quantification

Delivers quantitative measurements based on signal intensity

Comprehensive genetic information

Detects virtually all types of genomic DNA alterations, including single nucleotide variants, insertions and deletions, copy number changes, and chromosomal aberrations

Discovery power and flexibility

Offers flexibility to discover novel DNA variants, scale studies, and sequence multiple samples simultaneously

Common DNA sequencing methods

Whole-genome sequencing

Whole-genome sequencing is a comprehensive method for analyzing entire genomes. Rapidly dropping costs and the ability to produce large volumes of data with today’s sequencers make this method a powerful research tool.

Targeted resequencing

With targeted resequencing, a subset of genes or regions of the genome are isolated and sequenced, allowing scientists to focus time, expenses, and analysis on specific areas of interest.

Exome sequencing

This DNA sequencing method involves analyzing the protein-coding regions of the genome to uncover genetic influences on disease and population health.

Target enrichment

Target enrichment captures genomic regions of interest through hybridization and allows researchers to sequence large numbers of genes (typically > 50 genes) at once.

Methylation sequencing

Genome-wide and targeted DNA sequencing methods can provide researchers with insights into DNA methylation patterns at a single nucleotide level.

ChIP sequencing

Combining chromatin immunoprecipitation (ChIP) assays and sequencing, ChIP-Seq is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins.

MiSeq i100 sequencing start screen

Empowering access for groundbreaking genomic discoveries

Illumina benchtop sequencing systems are making NGS technology more accessible to laboratories worldwide. Learn how these systems provide the speed, power, and flexibility to make breakthroughs in microbiology, cancer research, and more.

Benchtop DNA sequencers

Compare the speed and throughput of Illumina DNA sequencing systems to find the best option for your lab.

Explore benchtop sequencers

Featured webinars

Capturing hidden meaning through multiomics

A key question driving interdisciplinary life science research is how to extract biological meaning from a wealth of genome-scale data. Scientists discuss integrated multiomic approaches that are uncovering “hidden” biological insights.

Evolving NGS technologies

Watch our webinar to hear from a panel of experts on how we are expanding what is possible with sequencing technology. Topics discussed include mapped read technology, Illumina 5-base solution, multiomics and multimodal assays, and bioinformatics.

Library prep for DNA sequencing

Library prep for DNA sequencing

The versatile Illumina library prep portfolio allows you to sequence small, targeted DNA regions or the entire genome. We've innovated in PCR-free and on-bead fragmentation chemistries, offering time savings, flexibility, and increased sequencing data performance.

Explore DNA library prep

Related solutions

Cancer DNA sequencing

NGS-based sequencing methods allow cancer researchers to detect rare somatic variants, perform tumor–normal comparisons, and analyze circulating DNA fragments.

Genotyping solutions

Sequencing- and array-based genotyping technologies can provide insight into the functional consequences of genetic variation.

Cell-free DNA sequencing

Cell-free DNA (cfDNA) are short fragments of DNA released into the bloodstream. cfDNA from maternal blood samples may be used to study common chromosomal conditions.

Microbial sequencing

Analysis of microbial species using DNA sequencing can inform environmental metagenomics studies, infectious disease surveillance, epidemiology research, and more.

FAQ

DNA sequencing is a scalable approach that is used to determine the order of nucleotides that make up a DNA molecule. The molecule consists of four distinct nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C). Identifying the sequence of these bases provides insights into the genetic information stored in a specific DNA segment.1

DNA sequencing workflows often include sample preparation or extraction, DNA fragmentation, PCR amplification or PCR-free approaches, followed by sequencing and data analysis. Common sequencing methods include Sanger sequencing and NGS. Sanger sequencing and certain NGS technologies use a DNA polymerase to incorporate fluorescently labeled nucleotides for base identification, but they differ significantly in chemistry and workflow.

Sanger sequencing is considered low throughput, as it sequences one DNA fragment at a time. In contrast, NGS enables parallel sequencing of millions of DNA fragments simultaneously.2

Learn more about the advantages of NGS vs. Sanger sequencing.

By determining the order of nucleotide bases, DNA sequencing enables scientists to address numerous biologically relevant questions. The data generated from DNA sequencing is commonly used in basic research to understand gene function, in forensics to identify individuals, and in medicine to help researchers better understand health and disease.

DNA sequencing turnaround times vary widely, from several hours for rapid targeted sequencing assays to days for more comprehensive whole-genome sequencing needs. Several factors determine DNA sequencing turnaround time, including the sequencing and processing methods used, as well as the operational capacity of the processing lab.3

Visit our sequencing platforms resource page to learn more about DNA sequencing run times.

Learn about whole-genome sequencing methods using NGS technology.

DNA sequencing faces both technical and biological challenges, including difficulties in sequencing GC-rich regions and highly repetitive sequences. Long-read sequencing technologies enable researchers to detect complex structural variants in the genome that are often difficult to analyze using short-read sequencing methods.4

Discover how our mapped read technology leverages on-flow cell library preparation and novel informatics that incorporate proximity information from clusters in neighboring nanowells to generate long-range genomic insights.

Learn more about the advantages of long-read sequencing for deeper insights into complex genomic regions.

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Additional resources

NGS technology

Discover the broad range of experiments you can perform with NGS, and find out how Illumina technology works.

Find the right kit

Determine the best library prep kit or array for your needs based on your starting material and method of interest.

Speak to a specialist

Talk to an expert to learn more about solutions for DNA sequencing.

References

  1. National Human Genome Research Institute. DNA Sequencing Fact Sheet. Genome.gov. genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Fact-Sheet. Published September 29, 2023. Accessed October 6, 2025. 
  2. Rodriguez R, Krishnan Y. The chemistry of next-generation sequencing. Nat Biotechnol. 2023;41(12):1709-1715. doi:10.1038/s41587-023-01986-3
  3. Armitage H. Fastest DNA sequencing technique helps undiagnosed patients find answers in mere hours. Stanford Medicine. med.stanford.edu/news/all-news/2022/01/dna-sequencing-technique.html. Published January 12, 2022. Accessed October 21, 2025. 
  4. Park J, Cook DE, Chang PC, et al. Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. Nat Biotechnol. Published online October 16, 2025. doi:10.1038/s41587-025-02839-x