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Long Read Sequencing

Genomic, transcriptomic and epigenetic characterization with high precision
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long read sequencing service header Continuous Long Read Sequencing

Why choose long read sequencing?

Next generation sequencing (NGS) technologies typically make use of generating 75-300bp long reads, which are then either de-novo assembled in a genome or mapped to a reference genome. Complex regulatory elements or highly repetitive sequences can make this mapping harder than for uniquely variable ones. With long read sequencing more than 100.000 bp long reads are assembled, making it easier to tackle:

  • Highly contiguous de novo assemblies
  • Sequencing through extended repetitive regions
  • Discovery of novel genes and novel isoforms of annotated genes

Long read sequencing is also frequently used in combination with short read sequencing.

long read sequencing advantages Continuous Long Read Sequencing
Mirjam Rademaker Continuous Long Read Sequencing
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PacBio (Pacific Biosciences) and Nanopore (Oxford Nanopore Technologies: ONT)

GenomeScan offers long read sequencing based on two distinct technologies, each with its own set of advantages.

Logo PacBio web Continuous Long Read Sequencing
  • Long read lengths up to ~25kb long for PacBio HiFi
  • Throughput per Sequel IIe SMRT cell: ~ 26 Gb, Revio SMRT cell: ~80 Gb
  • High read accuracy Q30 >99,9%
Logo ONT web Continuous Long Read Sequencing
  • Long read lengths up to > 4Mb
  • 1 PromethION Flowcell: ~100-200 Gb
  • Kit 14 Chemistry > Q20 (99%) for Simplex reads, ~Q30 (99.9%) for Duplex reads

Sequencing with PacBio

By utilizing SMRT technology, we are able to easily generate highly accurate (median consensus accuracy of >99.9%) long reads up to 30 kb (‘CCS or ‘HiFi’ reads). With reads tens of kilobases in length you can readily assemble complete previously uncharacterized genomes, sequence full-length transcripts as well as genes or regions of interest ranging in size from hundreds base pairs to 30 kb.

For this service we have available Sequel IIe and Revio System.

Revio System Sequel IIe System Increase
Higher density 25M ZMW 8M ZMW 3x
Independent stages 4 1 4x
Shorter run times 24hs 30hs 1.25x
 CCS data ~ 80Gb   ~20GB 4x

Additionally, calling and detection of variants benefit from long-read sequencing thanks to low sequencing-context bias, and accurate mapping of reads. Single Molecule, Real-Time (SMRT) Sequencing is a core technology and a powerful tool for analyzing variable number tandem repeats, or for repeat occurrence with disease significance, such as in Huntington’s disease.

  • Easier assembly of complete genomes
  • Sequencing full-length RNA transcripts
  • Direct detection of epigenetic modifications
  • Haplotype phasing information
  • Base-level resolution with >99.9% single-molecule read accuracy
  • Unbiased coverage of GC rich regions such as promoters
  • No PCR amplification, prevention of errors

How it works

Sequencing with Oxford Nanopore

Nanopore sequencing involves reading the code of single DNA/RNA strand as they are threaded through nanopores embedded within a membrane. As the DNA/RNA moves through the pore, the current is disrupted to produce a characteristic ‘squiggle’. The squiggle is then decoded using basecalling algorithms to determine the DNA or RNA sequence in real time.


  • Direct seq of DNA and RNA without using PCR: No bias, richer info including epigenetics.
  • Read length-agnostic: It’s able to seq different length of genome.
  • Real-time analysis: Rapid results, adaptive sampling, base calling at the same time its sequencing.
  • Chemistry on bespoke electronics: Scalable, from small to large formats.
ONT explanation 2 Continuous Long Read Sequencing

How it works

Which technology to choose

Nanopore’s defining feature is its real-time analysis, while PacBio promises high fidelity reads. If you are unsure about which technology suits your project the best, our specialists would be happy to help you.

In some cases, a hybrid sequencing strategy that combines different approaches (i.e. long read and short read sequencing) may be your perfect solution to answer complex questions.

Data analysis

GenomeScan’s bioinformatics experts apply optimized pipelines for preprocessing, assemblies, variant calling and disease annotations to analyze your dataset. With our customizable workflows, we help you receive reliable and publication-ready results.

Bioinformatic pipelines can also be tailored according to your research or clinical needs allowing more in-depth mining of your dataset.

Long Read Sequencing Resources



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Service workflow

long read sequencing product specification Continuous Long Read Sequencing
Service specifications

We have summarized key information about our long-read sequencing service into a service specification sheet.

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Other Services

Whole Genome Sequencing
Whole Exome Sequencing
Gene expression profiling
Single cell sequencing
Targeted proteomics panel

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