Detailed insight into complex genomes

Our technology uses an informatics method to assemble DNA fragments into synthetic long reads

Long-Read Sequencing Technology

Synthetic long-read sequencing technology is a highly accurate, end-to-end solution that can be used to:

  • Generate synthetic long reads for de novo assembly and genome finishing applications
  • Sequence traditionally challenging genomes, such as those containing stretches of highly repetitive elements
  • Perform whole human genome phasing to identify co-inherited alleles, haplotype information, and phase de novo mutations
Push-Button Informatics

Our user-friendly software tools make NGS data analysis accessible to any researcher, regardless of bioinformatics experience.

Learn More
Explore the NovaSeq 6000 System

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

Learn More
Explore the NovaSeq Series

Moleculo, acquired by Illumina in late 2012, developed an innovative technology for generating long reads that combines a new library prep method and genome analysis tools. The technology breaks DNA into large fragments that are sequenced on standard Illumina sequencing platforms for subsequent assembly into synthetic long reads or whole human genome phasing using proprietary informatics.

Illumina synthetic long-read technology begins by fragmenting genomic DNA to approximately 10 kilobases. Next, these fragments are clonally amplified, sheared, and marked with a unique barcode. They are then sequenced with Illumina technology.

The short sequence reads originating from each molecule are assembled into synthetic long reads, or long fragments. These fragments assign haplotype information to homologous chromosomes in the phasing application. The fragments are also used for genome finishing or de novo sequencing in the long read application.

Synthetic long-read sequencing technology has the potential to improve the efficiency and accuracy of many existing DNA sequencing applications while increasing the coverage of clinically important genes. These advantages allow for the phased re‐sequencing of human genomes and rapid de novo sequencing of plant and animal genomes.

The long reads produced typically span more than one heterozygous SNP in the phasing application. A proprietary phasing algorithm "stitches" multiple long reads into a single haplotype and thus phases the genome.

The technology simplifies de novo sequencing because large repeat regions in the DNA fragments can easily be spanned.

Learn more about:

The Illumina Long-Read Applications Ecosystem is a group of partnerships dedicated to ensuring the delivery of high-quality data for a fully featured genome, including phasing, detection of structural variants, and de novo assembly of all species. We believe that the combination of our core sequencing technology, along with our partners’ linked-read preps, assembly protocols, and analysis pipelines, will enable Illumina to bring advanced long read applications solutions to the market today. The Illumina Long-Read Ecosystem leverages the following partner products and services.

Long-Read Sequencing Partnerships
10x Genomics
10x Genomics

10x Genomics Chromium genome and exome products, making phasing and structural variant information accessible to our human health researchers.

Learn More

Dovetail Genomics

Dovetail Genomics assembly service (full assembly and assembly improvements) for a wide range of genomes, leveraging its Chicago library prep and proprietary analysis pipeline.

Learn More


NRGene DeNovoMagic analysis product, delivering computational tools to facilitate optimal trait discovery for seed companies, animal breeders, and academia.

Learn More
Interested in receiving newsletters, case studies, and information from Illumina based on your area of interest? Sign up now.