Population genomics

The advent of high-throughput genomic analysis technologies has driven the field of population genomics — the large-scale comparison of genomes within a population. Population genomics has been fundamental to the identification of novel variation that can define specific phenotypes, such as disease susceptibility; however, the technical limitations of traditional analysis platforms may miss important sources of genomic variation. Combining long sequencing reads (up to 4 Mb) with high sample throughput (up to 14 Tb on PromethION*) nanopore technology makes it possible to generate highly contiguous genomes, with resolution and phasing of single nucleotide variants (SNVs), structural variants (SVs), repeats, and DNA methylation in a single assay — across 10s to 1,000s of samples.

We've developed an efficient and scalable wet lab and computational protocol for nanopore long-read sequencing that [serves as a] genuine alternative to short reads for large-scale genomic projects

Kimberley Billingsley, NIH CARD, USA

Technology comparison

Oxford Nanopore sequencing

Traditional short-read technologies

Comprehensive genomic characterisation

Limited genomic characterisation

Short sequencing reads do not typically span important classes of genomic aberrations such as large structural variants and repeat regions, instead relying on indirect inference and/or complex computational analyses for their detection. The requirement of traditional sequencing technologies for amplification can also introduce sequence bias and removes base modifications. As a result, only a fraction of the genomic variation present in a sample may be identified.

Flexible and on demand

  • Scalable, affordable devices to suit all genome and project sizes
  • Generate terabases of data with PromethION — use up to 48 high-capacity flow cells simultaneously or independently to match your sample availability and lab requirements
  • Sequence smaller genomes at high throughput or perform low-pass sequencing of larger genomes with GridION
  • Discover the advantages of nanopore sequencing and undertake pilot projects with MinION, at just $1,999, including flow cells and sequencing reagents
  • Perform sample QC prior to large-scale studies using Flongle, with flow cells at $90 each

Limited flexibility

Traditional high-throughput benchtop sequencing devices require significant infrastructure requirements and expense — confining their use to well-resourced, centralised locations. Sample batching is often required for optimal efficiency, potentially leading to long turnaround times.

Streamlined workflows

  • Prepare DNA samples for sequencing in as little as 10 minutes, including multiplexing
  • Easy-to-automate sample preparation kits and protocols suitable for large-scale population genomics projects
  • Low DNA input requirements
  • Run multiple analyses — whole-genome, targeted, and full-length RNA sequencing — on a single device and at the same time, with modular PromethION and GridION

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency and increasing turnaround times.

Real-time data streaming

  • Analyse data as it is generated for immediate insights
  • Gain enhanced coverage of specific genomic regions with real-time targeted sequencing using adaptive sampling
  • Stop sequencing when sufficient data generated — wash and reuse flow cell

Fixed run time with bulk data delivery

Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional practical complexities of handling large volumes of bulk sequence data.

White paper

New insights into large genomes

Discover how researchers worldwide are utilising long nanopore sequencing reads to support the generation of highly accurate and contiguous, chromosome-level genome assemblies across many different species. With the facility to generate read lengths in excess of 4 Mb, nanopore sequencing reads enable complete resolution of challenging genomic regions, allowing identification of previously hidden genomic variation — providing new insights into evolution and disease association.

Find more publications on the use of nanopore sequencing for large-scale population genomics studies in our Resource centre.


Accelerating clinical research with high-throughput whole-genome nanopore sequencing

The analysis of large cohorts of clinical research samples is critical to advancing our understanding of the mechanisms of disease and identifying novel biomarkers. Find out how nanopore whole-genome sequencing on the PromethION 24 enables the comprehensive characterisation of genomic and epigenomic variants in up to 2,496 human genomes per year in our end-to-end workflow.

Case study

Capturing global genomic diversity in the human pangenome with long nanopore reads

Though the human reference genome has been a valuable resource in scientific research for the past 20 years, it is fundamentally limited by its representation of such a small proportion of genetic diversity. To address this, the Human Pangenome Reference Consortium utilised nanopore sequencing data in their development of the first human pangenome reference, including data from people with diverse backgrounds to represent a broader range of genetic diversity.

in the future, the combination of the pangenome and low-cost long-read sequencing should prove to be a potent combination for comprehensive SV genotyping

Liao et al., Nature (2023)

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Scalable sequencing for population genomics

Nanopore sequencing is uniquely scalable — from portable Flongle and MinION devices, ideal for sample QC and pilot studies, through to the high-throughput benchtop GridION and PromethION platforms, which offer rapid and affordable access to the high outputs of high-quality data required for large-scale population genomics projects.

Recommended for population genomics

PromethION 48

Combining up to 48 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 48 delivers flexible, on-demand access to terabases of sequencing data — ideal for large-scale population genomics projects.


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