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Long-read sequencing

PacBio’s single molecule real time (SMRT) long read sequencing generates the highest quality sequencing data available.

Long-read sequencing technologies enable the analysis of genomic and transcriptomic features that are difficult or impossible to resolve using short-read sequencing alone. By generating reads that span thousands to tens of thousands of bases, long-read platforms provide improved resolution of complex genomic regions and long-range structural variation.

 

Applications that commonly benefit from long-read sequencing include:

  • De novo genome assembly

  • Detection of large and structural variants

  • Resolution of repetitive genomic regions

  • Full-length transcript sequencing to characterise isoform diversity

  • Epigenetic analysis, including detection of DNA modifications

  • Population sequencing and analysis of complex samples, such as viral communities

  • Metagenomic studies, including assembly of metagenome-assembled genomes (MAGs)

The Centre for Genomic Research provides access to two complementary long-read sequencing technologies: PacBio HiFi sequencing and Oxford Nanopore sequencing. Each platform offers distinct advantages depending on project goals, sample characteristics, and experimental design.

 

PacBio Long-Read Sequencing

PacBio long-read sequencing at the Centre for Genomic Research supports projects requiring highly accurate long reads and comprehensive genome resolution, including de novo genome assembly, isoform characterisation, and structural variant detection.

CGR provides expert consultation, high-quality PacBio library preparation, and access to the PacBio Revio platform, which offers significantly increased throughput and efficiency compared with previous Sequel II systems, enabling larger-scale and more efficient long-read projects.

In addition, the PacBio Ampli-Fi library preparation protocol allows users to generate high-quality long-read data from low-input DNA (as little as 10 ng), removing the traditional requirement for large amounts of input DNA and expanding access to long-read sequencing for limited or precious samples.

PacBio HiFi reads combine long read lengths with very high per-read accuracy, making the technology particularly well suited to applications such as high-quality genome assembly, structural variant analysis, and full-length transcript sequencing.

 

Oxford Nanopore Long-Read Sequencing

Oxford Nanopore sequencing provides flexible long-read sequencing for projects requiring extended read lengths, real-time data generation, and direct analysis of native DNA or RNA molecules. The technology can produce reads ranging from several kilobases to ultra-long fragments, enabling the analysis of genomic regions that are difficult to resolve using other sequencing approaches.

The Centre for Genomic Research operates an Oxford Nanopore PromethION P2 platform, supported by dedicated compute infrastructure for data acquisition, basecalling, and downstream analysis. This platform delivers high-throughput long-read sequencing suitable for a wide range of research applications while supporting efficient processing of both pilot studies and larger-scale projects.

Because molecules are sequenced directly as they pass through a nanopore, the technology also enables direct detection of nucleotide modifications, such as DNA methylation, without the need for additional chemical treatment or specialised library preparation workflows.

Oxford Nanopore sequencing is particularly well suited to applications requiring ultra-long reads, rapid data generation, or the analysis of native DNA and RNA molecules.

 

Choosing the Right Long-Read Approach

PacBio and Oxford Nanopore technologies offer complementary strengths. PacBio HiFi sequencing provides highly accurate long reads well suited to applications such as high-quality genome assembly and structural variant detection, while Oxford Nanopore sequencing offers flexible long-read generation, ultra-long reads, and direct detection of nucleotide modifications.

The most appropriate technology depends on the specific aims of each project, as well as factors such as genome size, sample quality, and desired data outputs.

Researchers interested in long-read sequencing are encouraged to contact us to arrange a consultation, where our team can help assess project requirements and advise on the most appropriate sequencing strategy.