A comprehensive view of complex genomes

A base-by-base view of genomic alterations to inform studies of disease or population genomics

Large Whole-Genome Sequencing

Sequencing large genomes (> 5 Mb) can provide valuable information for disease and population-level studies. Researchers often use large whole-genome sequencing to analyze tumors, investigate causes of disease, select plants and animals for agricultural breeding programs, and identify common genetic variations among populations.

Large Whole-Genome Sequencing in 3 Steps

Obtain a base-by-base view of genomic alterations with this simple workflow solution.

View Recommended Workflow  

  • Provides a high-resolution, base-by-base view of the genome
  • Combines short inserts and longer reads to allow characterization of any genome
  • Reveals disease-causing alleles that might not have been identified otherwise
  • Identifies potential causative variants for further follow-on studies of gene expression and regulation mechanisms

Analyzing the whole genome using next-generation sequencing (NGS) delivers a base-by-base view of all genomic alterations, including single nucleotide variants (SNV), insertions and deletions, copy number changes, and structural variations. Paired-end whole-genome sequencing involves sequencing both ends of a DNA fragment, which increases the likelihood of alignment to the reference and facilitates detection of genomic rearrangements, repetitive sequences, and gene fusions.

Sequencing Method Explorer

Use this interactive tool to explore experimental next-generation sequencing (NGS) library preparation methods compiled from the scientific literature.

Find a Method
Sequencing Method Explorer

Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*

In addition to our industry-leading data quality, Illumina offers integrated workflows that simplify the entire process, from library preparation to data analysis.

Click on the below to view products for each workflow step.

Nextera DNA Flex Library Prep Kit

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

TruSeq DNA PCR-Free Library Prep Kit

Library preparation for whole-genome sequencing of any species without PCR-induced bias.

TruSeq Nano DNA Library Prep Kit

Efficient library preparation from samples with limited available DNA, delivering high coverage quality and reduced bias.

Nextera Mate Pair Library Prep Kit

Gel-free and gel-plus methods for preparing mate pair libraries for sequencing from low DNA input.

Library Prep Kit Selector

Determine the best kit for your needs.

NextSeq 550 System

Flexible power to sequence the genome, exome, or transcriptome of any species, including up to 1 human genome per run.

HiSeq 4000 System

High throughput and low cost for production-scale genomics, sequencing up to 12 large genomes per run.

HiSeq X Series

$1000 human genome and ultra-high throughput for population-scale sequencing of up to 18,000 genomes per year.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Sequencing Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents and Flow Cells

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

BaseSpace Whole-Genome Sequencing App

Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.

BaseSpace Tumor-Normal App

Enables researchers to detect somatic variants from a tumor and matched normal sample pair.

BaseSpace Variant Interpreter

Leverages leading annotation databases and a powerful filtering interface to identify disease-associated variants rapidly.

Integrative Genomics Viewer

Associates single gene or list of genes with annotation data for pathways, diseases, tissues, and small molecules.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

The NovaSeq S4 Flow Cell is Here

Reagent kits for the NovaSeq 6000 System are now available in three flow cell configurations: S1 is ideal for smaller batch sizes or in situations where rapid turnaround time is required. S2 is a quick, powerful, and cost-effective option for high-throughput applications. S4 offers tunable output and additional flexibility.

View Kits
The NovaSeq S4 Flow Cell is Here
Sequencing Cancer Genomes
Cancer Whole Genome Sequencing

Whole-genome sequencing of tumor and matched normal tissue samples provides a comprehensive view of the unique mutations in cancer, informing studies of oncogenes and other risk factors. Learn more about cancer genome sequencing.

Causal Variant Studies
Causal Variant Discovery

Whole human genome sequencing can identify single nucleotide variants and copy number variations associated with disease. Identifying these causal variants can help researchers characterize disease mechanisms. Learn more about causal variant discovery.

Plant and Animal Sequencing
Plant and Animal Sequencing

Whole-genome sequencing of plants and animals is an efficient approach for discovering genes, SNPs, and structural variants. This information can improve breeding and selection in agriculture. Learn more about plant and animal sequencing.

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Whole-Genome Sequencing with the NextSeq Series
Whole-Genome Sequencing with the NextSeq Series

The NextSeq Series of sequencing systems offers an accessible whole-genome sequencing workflow solution.

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Sequencing to Understand Age-Related Diseases
Sequencing to Understand Age-Related Diseases

Human Longevity, Inc. aims to address challenges related to aging and disease through the power of population genomics.

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Paired-End Sequencing
Paired-End Sequencing

Paired-end sequencing facilitates detection of genomic rearrangements and repetitive sequence elements.

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Modern breeding programs for sunflower farming
Modern Breeding Programs for Sunflower Farming

The sunflower industry adopts genomics tools to better inform breeding decisions and improve disease resistance.

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Feline Social Media Star Gets Sequenced
Feline Social Media Star Gets Sequenced

Researchers crowdfunded the genome sequencing of Lil Bub to uncover the genetic causes of the cat's rare diseases.

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NGS to Study Genetics of Brain Development
NGS to Study Genetics of Brain Development

Researchers apply functional genomic methods to identify the role of gene variants in intellectual disability.

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Shared Vision for the Power of Human WGS
Shared Vision for the Power of Human WGS

Genomics leaders share their perspective on the impact of high-throughput and population sequencing in clinical research.

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*Data calculations on file. Illumina, Inc., 2015