Long-Read Sequencing Technology

What is long-read sequencing?

Long-read sequencing is a DNA sequencing approach 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 in the genome 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.

Advantages of long-read sequencing

Long-read sequencing 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 technology innovations

We have a broad range of innovations in development, including constellation mapped read technology, which uses a highly simplified NGS workflow that enables on-flow cell library prep and standard short-reads with cluster proximity information.

View innovation roadmap

Introducing Illumina Complete Long Read 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

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Introducing Illumina Complete Long Read sequencing technology

How long-read sequencing technology works

Illumina Complete Long Read technology uses tagmentation 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 sequences 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 sequencing technologies have laborious workflows as well as 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 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.

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Alternative long-range genomics technology: Linked reads

Transposase enzyme-linked long-read sequencing (TELL-Seq) technology uses linked reads to generate 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 with TELL-Seq

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

Microbial de novo assembly with TELL-Seq

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

Insect genome assembly with TELL-Seq

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.

Deeper insights into complex genomic regions with long reads