Whole-Genome Sequencing


For whole-genome sequencing, the combination of short inserts and longer reads allow characterization of any genome. For de novo whole-genome sequencing, the unparalleled raw read accuracy of Illumina next-generation sequencing (NGS) technology provides high quality, long contig assemblies.

Library Generation for Whole-Genome Sequencing

The Illumina whole-genome sequencing workflow starts with the generation of sequencer-ready DNA fragment libraries from genomic DNA. Illumina offers two basic options:

  • For human or other complex whole genome preparation: We recommend the TruSeq DNA family. This includes the PCR-Free and Nano kits.
  • For rapid genome preparation: We recommend the Nextera family. This includes the Nextera XT Kit, suitable for small genomes such as bacteria and viruses.

Phased Sequencing Complements Whole-Genome Sequencing

Phased sequencing complements human whole-genome sequencing by providing distinct gene information from homologous chromosomes, supporting haplotyping and allele-specific solutions. It enables researchers to distinguish between maternally and paternally inherited alleles.

Whole-Genome Sequencers and Data Analysis Solutions

Illumina offers a broad range of instruments and informatics solutions that enable whole genome sequencing of any genome, from small microbial genomes to large complex genomes.

Related Solutions

Desktop Genome Sequencer


The NextSeq 500 System can sequence a whole human genome at high coverage (30×) in one run.
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Library Prep Kit Selector

Product Selector

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Whole-Genome Sequencing of Complex Microbial Mixtures

Use metagenomic sequencing to analyze microbial populations, including unculturable microbes.


Featured Products & Services

TruSeq DNA PCR-Free Library Preparation Kit
TruSeq DNA PCR-Free Library Preparation Kit

Shortened library prep workflow for whole genome sequencing applications.

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TruSeq Nano DNA Library Prep Kit
TruSeq Nano DNA Library Prep Kit

Enables efficient interrogation of samples with limited available DNA.

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Nextera XT Sample Prep Kit
Nextera XT Library Prep Kit

Enables the fastest and easiest whole-genome library preparation method for sequencing small genomes, amplicons, and plasmids.

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The BaseSpace NGS Data Analysis environment offers simple analysis and sharing of whole-genome sequencing data produced on Illumina sequencers.

The BWA Whole-Genome Sequencing and Isaac Whole-Genome Sequencing BaseSpace Apps simplify data analysis for large genome sequencing.

Integrative Genomics Viewer (IGV) is a genome browser developed by the Broad Institute that displays next-generation sequencing data.



The Illumina Genome Network offers human whole-genome sequencing services.