Long-Read Sequencing Technology

Deeper insights into complex regions of the genome

Long-read sequencing helps reveal the most challenging regions of the genome

What is long-read sequencing?

Long-read sequencing is a DNA sequencing technique that enables the sequencing of much longer DNA fragments than traditional short-read sequencing methods. While short reads can capture the majority of genetic variation, long-read sequencing allows the detection of complex structural variants that may be difficult to detect with short reads. These include large inversions, deletions, or translocations, some of which have been implicated in areas like genetic disease.

Long-read technology can help resolve challenging regions of the genome by sequencing thousands of bases to:

  • Resolve traditionally difficult to map genes or regions of the genome, such as those containing high variable or highly repetitive elements
  • Perform phased sequencing to identify co-inherited alleles, haplotype information, and phase de novo mutations
  • Generate long reads for de novo assembly and genome finishing applications
Illumina Complete Long Reads

Introducing Illumina Complete Long Read sequencing technology

  • Generates contiguous long-read sequences with N50 of 5–7 kb with some reads > 10 kb
  • Provides a streamlined, robust, and cost-effective workflow compatible with all NovaSeq systems, giving you access to both long- and short-read data on a single instrument
  • Leverages the accuracy and speed of DRAGEN analysis with the ease of BaseSpace Sequence Hub apps

Learn More

Introducing Illumina Complete Long Read sequencing technology
How the Illumina Complete Long Read technology works

Tagmentation is used to normalize long fragment sizes. Long fragments are “land-marked” to capture single-molecule, long-read information and amplified. Marked fragments are tagmented to standard libraries for sequencing. Marked and unmarked data from standard short-read genome are combined to generate highly accurate long reads.

Long-read and short-read sequencing

It can be advantageous to combine long-read data with complementary short-read information. Many long-read solutions have laborious workflows and highly variable results.1-4 Short reads (typically 50–600 bp) offer high data quality and sequence depth at low cost. With advanced data analysis, short-read sequencing can generate whole-genome variant calls with outstanding accuracy. In addition, a small fraction of genic regions can benefit from long-read information to improve resolution of the most difficult-to-map genes.

Improved genome sequencing and human phasing

Long-read sequencing technology has the potential to improve the efficiency and accuracy of some existing DNA sequencing applications while increasing the resolution 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. The technology simplifies de novo sequencing because large repeat regions in the DNA fragments can easily be spanned.

Alternative long-range genomics technology: Linked reads

Linked reads are an alternative technology that generates non-contiguous, long-range data to inform de novo assembly or ultra-long distance (> 1 Mb) phasing. This alternative sequencing data type can be used to complement standard short reads for novel or complex genomes.

Ultra-long-range phasing

TELL-Seq technology generates ultra-long phasing blocks, providing an accessible solution to perform genome phasing studies.

Microbial de novo assembly

TELL-Seq demonstrates exceptional performance for microbial WGS, even for challenging samples or regions with high GC content.


Learn how researchers use transposase enzyme-linked long-read sequencing (TELL-Seq) to sequence and assemble genomes of nine insect species in this recorded webinar.

Related applications

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Rare disease whole-genome sequencing

Whole-genome sequencing is the most comprehensive test for rare disease, with the potential for superior diagnostics and outcomes.

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Human whole-genome sequencing

Human whole-genome sequencing provides the most detailed view into the complex genetic variants that make us unique.

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Cancer whole-genome sequencing

Get a comprehensive base-by-base view of the unique genomic abnormalities in cancer.

Related Solutions

Sequencing Platforms

Compare next-generation sequencing (NGS) platforms by application, throughput, and other key specs. Find tools to help you choose the right sequencer.

Technological Advancements

Read articles about recent genomics breakthroughs and advances in bioinformatics and clinical research from Illumina scientists and thought leaders.

DNA Sequencing

During DNA sequencing, the bases of a fragment of DNA are identified. Illumina DNA sequencers can produce terabases of sequence data from a single run.

  1. Pacific Biosciences. Preparing DNA for PacBio HiFi sequencing—Extraction and quality control. pacb.com/wp-content/uploads/Technical-Note-Preparing-DNA-for-PacBio-HiFi-Sequencing-Extraction-and-Quality-Control.pdf.
  2. Pacific Biosciences. Preparing whole genome and metagenome libraries using SMRTbell prep kit 3.0. pacb.com/wp-content/uploads/Procedure-checklist-Preparing-whole-genome-and-metagenome-libraries-using-SMRTbell-prep-kit-3.0.pdf.
  3. Oxford Nanopore Technologies. Ligation Sequencing Kit. store.nanoporetech.com/us/ligation-sequencing-kit110.html.
  4. Pacific Biosciences. Low Yield Troubleshooting Guide. pacb.com/wp-content/uploads/Guide-Low-Yield-Troubleshooting.pdf.