Whole-genome sequencing

Generate reference-quality microbial, human, animal, and plant genome assemblies with long nanopore sequencing reads (reads >4 Mb demonstrated). The greater overlap offered by long reads enhances genome assembly by providing longer continuous, unambiguously assembled sequences, resulting in fewer contigs. Accurately resolve structural variants and repeat regions, and characterise base modifications (e.g. methylation), fusion genes, and haplotype phasing, with PCR-free nanopore sequencing data.

Introduction

What is whole-genome sequencing?

Whole-genome sequencing aims to provide complete analysis of an organism’s genome. The technique allows subsequent reassembly of the genome sequence and identification of novel variants and genomic structures that would be missed by targeted sequencing approaches. Until recently, routine application of whole-genome sequencing was limited due to its comparatively high cost; however, the development of modern sequencing techniques, such as nanopore sequencing, now enable every researcher to benefit from comprehensive and cost-effective whole-genome characterisation of their samples of interest.

Whole-genome sequencing has been instrumental in many research areas, from identifying novel disease-associated variation in humans, plants, and animals, to tracking microbial outbreaks such as SARS-CoV-2.

Loading a PromethION Flow Cell
Nanopore sequencing devices

Why nanopore technology for whole-genome sequencing?

Nanopore technology delivers the most comprehensive whole-genome analysis available on a single platform.

Using nanopore sequencing, you can:

  • Resolve structural variants, repeat regions, and phased haplotypes with ultra-long reads
  • Generate reference-quality, telomere-to-telomere genome assemblies
  • Eliminate amplification bias and identify epigenetic modifications as standard
  • Streamline your workflow with 10-minute library prep and real-time data streaming
  • Scale to your needs — using Flongle, MinION, GridION, or PromethION

Experimental approach to whole-genome sequencing

A wide range of library preparation kits are available to suit all whole-genome sequencing requirements. Amplification-free kits allow direct, long-read sequencing of native DNA, eliminating the potential for PCR bias and enabling the detection of base modifications (e.g. methylation) alongside the nucleotide sequence. Amplification-based kits are also available, enabling whole-genome sequencing from low input amounts or poor-quality DNA (e.g. FFPE samples).

Application-free, native DNA sequencing and retained base modification Amplification-based for low DNA amounts or quality
Ligation Sequencing Kit Rapid Sequencing Kit Ultra-Long Sequencing Kit Rapid PCR Barcoding Kit
Preparation time 60 min 10 min 200 min + O/N elution 15 min + PCR
Input requirement 1,000 ng gDNA; 100–200 fmol amplicons or cDNA 100 ng gDNA (<30 kb) 6 M cells 1–5 ng gDNA
Fragmentation Optional Transposase based Transposase based Transposase based
Read length Equal to fragment length Random distribution, dependent on input fragment length 50–100+ kb N50 ~2 kb
Typical throughput 3/3 2/3 2/3 2/3
Multiplexing options 24 plex, 96 plex 24 plex, 96 plex - 12 plex
Methylation included Yes Yes Yes -
Overview Optimised for output; retained base modifications; control over read length Simple and rapid; retained base modifications Optimised for production of ultra-long reads (N50 ≥50 kb); retained base modifications Simple and rapid
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Get started with whole-genome sequencing

Get best practice recommendations to optimise your end-to-end whole-genome sequencing workflow in our Getting started guides.

Sequencing devices

Which device for whole-genome sequencing?

From portable, yet powerful Flongle and MinION devices, suitable for microbial genomes, through to the flexible GridION device and high-output PromethION devices, ideal for large eukaryotic genomes — scale your sequencing to match your specific whole-genome sequencing requirements.

  • Theoretical max output (TMO). Assumes system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Actual output varies according to library type, run conditions, etc. TMO noted may not be available for all applications or all chemistries.
Recommended for whole-genome sequencing

PromethION 2 and PromethION 2 Solo

Offering the flexibility of two independent, high-output PromethION Flow Cells, the compact PromethION 2 devices bring the benefits of high-coverage, real-time nanopore sequencing to every lab. Ideal for low-cost access to highly accurate whole genome and metagenome assemblies.

Analysis techniques for whole-genome sequencing

Analysis solutions

A wide range of pipelines and tools are available for the analysis of nanopore whole-genome sequencing data, enabling accurate analysis of large and small variants, plus the generation of highly contiguous genome assemblies. Best practice analysis pipelines for small genome assembly and human variant calling, amongst many others, are available in EPI2ME Labs.

Find out more about analysing nanopore whole-genome sequencing data.

Featured whole-genome sequencing workflow

For high-throughput analysis of human genomes, we recommend the following:

Inspiration for whole-genome sequencing

Discover more about applying nanopore whole-genome sequencing to your organism and genomic variants of interest.

Research areas

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