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. Today, researchers 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 Simple Steps

Obtain a base-by-base view of genomic alterations with this seamless 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.

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 DNA Library Prep Kit

An easy-to-use system for preparing high-quality NGS libraries compatible with all Illumina sequencing platforms.

Nextera Mate Pair Library Prep Kit

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

TruSeq Synthetic Long-Read DNA Library Prep Kit

Highly accurate assembly of long sequencing reads from shorter reads for whole-genome sequencing or genome phasing.

Find the Right Whole-Genome Library Prep Kit

Determine the best kit for your needs.

NextSeq Series

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

HiSeq 2500 System

Production power and efficiency to sequence up to 10 large genomes per run.

HiSeq 3000/HiSeq 4000 Systems

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

HiSeq X Series

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

NovaSeq Series

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

Platform Comparison Tool

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

Sequencing Reagents

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

BWA Whole-Genome Sequencing App

Processes whole-genome sequencing data using BWA alignment and GATK variant calling.

Isaac Whole-Genome Sequencing App

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

Tumor-Normal App

Detects 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.

The Broad’s IGV

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.

Cancer Genome Sequencing
Cancer Whole Genome Sequencing

Sequencing tumor and matched normal tissue provides a comprehensive view of the unique mutations in cancer, informing studies of oncogenes and other risk factors. Learn more about cancer whole-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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Paired-End Sequencing
Paired-End Sequencing

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

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