Whole-Genome Sequencing (WGS)

What is Whole-Genome Sequencing?

Whole-genome sequencing (WGS) is a comprehensive method for analyzing entire genomes. Genomic information has been instrumental in identifying inherited disorders, characterizing the mutations that drive cancer progression, and tracking disease outbreaks. Rapidly dropping sequencing costs and the ability to produce large volumes of data with today’s sequencers make whole-genome sequencing a powerful tool for genomics research.

While this method is commonly associated with sequencing human genomes, the scalable, flexible nature of next-generation sequencing (NGS) technology makes it equally useful for sequencing any species, such as agriculturally important livestock, plants, or disease-related microbes.

Advantages of Whole-Genome Sequencing

  • Provides a high-resolution, base-by-base view of the genome
  • Captures both large and small variants that might be missed with targeted approaches
  • Identifies potential causative variants for further follow-up studies of gene expression and regulation mechanisms
  • Delivers large volumes of data in a short amount of time to support assembly of novel genomes

An Uncompromised View of the Genome

Unlike focused approaches such as exome sequencing or targeted resequencing, which analyze a limited portion of the genome, whole-genome sequencing delivers a comprehensive view of the entire genome. It is ideal for discovery applications, such as identifying causative variants and novel genome assembly.

Whole-genome sequencing can detect single nucleotide variants, insertions/deletions, copy number changes, and large structural variants. Due to recent technological innovations, the latest genome sequencers can perform whole-genome sequencing more efficiently than ever.

Compare Whole-Genome & Exome Sequencing

Explore the benefits of each approach to determine which method is best for your research.

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Key Whole-Genome Sequencing Methods

Large Whole-Genome Sequencing

Sequencing large genomes (> 5 Mb), such as human, plant, or animal genomes, can provide valuable information for disease research and population genetics.

Small Whole-Genome Sequencing

Small genome sequencing (≤ 5 Mb) involves sequencing the entire genome of a bacterium, virus, or other microbe. Without requiring bacterial culture, researchers can sequence thousands of small organisms in parallel using NGS.

De Novo Sequencing

De novo sequencing refers to sequencing a novel genome where there is no reference sequence available. NGS enables fast, accurate characterization of any species.

Phased Sequencing

Phased sequencing, or genome phasing, distinguishes between alleles on homologous chromosomes, resulting in whole-genome haplotypes. This information is often important for genetic disease studies.

Human Whole-Genome Sequencing

Previously a challenging application, human whole-genome sequencing has never been simpler. It offers the most detailed view into our genetic code.


Whole-Genome Sequencing Data Analysis

The DRAGEN Bio-IT Platform provides accurate, ultra-rapid analysis of NGS data, including WGS data. The platform can process data for an entire human genome at 30× coverage in about 25 minutes.

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How Scientists Use WGS

Investigating the Genetics of COVID-19 Susceptibility

Illumina is providing whole-genome sequencing for a UK-wide study led by Genomics England, designed to compare the genomes of severely and mildly ill COVID-19 patients.

The Time is Now for Microbiome Studies

Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.

Analyzing Leukemia Samples with WGS

A New England Journal of Medicine study found that using WGS to assess leukemia samples produced more accurate results, in less time, than karyotyping or fluorescence in situ hybridization.

Featured Products

Illumina DNA Prep
Illumina DNA Prep

A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.

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NovaSeq 6000 Reagent Kit
NovaSeq 6000 Reagent Kit

Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.

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MiSeq Reagent Kit
MiSeq Reagent Kit

Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier MiSeq reagent kit versions.

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BaseSpace Sequence Hub and iCredits
BaseSpace Sequence Hub and iCredits

Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing operations.

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Exploring the Genetics of Neuropsychiatric Disease

Dr. Kristen Brennand discusses how integrating whole-genome sequencing data with transcriptome and epigenetic information in tissues of interest can help identify genes and pathways that have a role in particular diseases.

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Related Solutions

Cancer Whole-Genome Sequencing

Whole-genome sequencing of tumor samples provides a comprehensive view of the unique mutations in cancer tissue, informing analysis of oncogenes, tumor suppressors, and other risk factors.

Microbial Whole-Genome Sequencing

This method can be utilized to generate accurate microbial reference genomes, identify novel bacteria and viruses, perform comparative genomic studies, and more.

Shotgun Metagenomics

This method allows researchers to identify the organisms present in a given complex sample, analyze bacterial diversity, and detect microbial abundance in various environments.

Noninvasive Prenatal Testing

NGS-based WGS involves analysis of cell-free DNA fragments across the entire genome, which has proven advantages over other prenatal testing methodologies.

Rare Disease Whole-Genome Sequencing

This method can detect multiple variant types in a single assay, and help clinical researchers identify causative genetic variants linked to rare disorders.

Complex Disease Research

Researchers can utilize WGS and other methods to identify genetic variants associated with complex diseases and characterize disease mechanisms.

COVID-19 Host Risk and Immune Response

Understanding host genetic differences and individual immune responses to the SARS-CoV-2 virus increases understanding of disease susceptibility and severity. Read more about methods for studying these differences, from WGS to RNA-Seq, methylation arrays, and more.

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Additional Tips and Training Opportunities

Find Content and Products for Your Field

The user-friendly "Recommended Links" feature allows you to quickly find in-depth content and products relevant to your specific field of interest. You can access this option from the top of any illumina.com page.

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What is the PhiX Control v3 Library?

This library is derived from the small, well-characterized bacteriophage genome, PhiX. It is an ideal sequencing control for run quality monitoring.

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Additional Resources

Sequencing Platforms
Sequencing Platforms

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Pharmaceutical Scientist in Lab
CYP2D6 Genotyping Using WGS Data

WGS offers a promising option for building accurate drug-metabolizing enzyme allele frequency databases for pharmacogenomics.

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Library Prep and Array Kit Selector
Library Prep and Array Kit Selector

Determine the best kit for your needs based on your project type, starting material, and method of interest.

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Sequencing Services

Sequencing Services

Find high-quality whole-genome and other sequencing services that deliver analyzed data to researchers.

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Sequencing Method Explorer
Sequencing Method Explorer

Use this interactive tool to explore experimental NGS library preparation methods compiled from the scientific literature.

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View Sequencing Coverage Tips
View Sequencing Coverage Tips

Learn how to estimate and achieve the necessary sequencing coverage for your experiment.

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