Whole-genome sequencing

Nanopore technology provides a more accurate whole-genome sequencing technique than legacy technologies. Generate reference-quality microbial, human, animal, and plant genome assemblies with long nanopore reads (>4 Mb achieved). Long reads enhance genome assembly by offering greater sequencing overlap, providing longer continuous, unambiguously assembled sequences and fewer contigs. Use PCR-free nanopore sequencing workflows to accurately resolve structural variants and repeat regions, characterise base modifications and fusion genes, and phase haplotypes — all on a single platform.


What is whole-genome sequencing?

Whole-genome sequencing aims to provide complete analysis of an organism’s genome. The technique allows subsequent assembly 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.

Loading a PromethION Flow Cell

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:

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.

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, such as methylation, alongside the nucleotide sequence without additional sample prep. Amplification-based kits are also available, enabling whole-genome sequencing from low input amounts or poor-quality DNA, such as FFPE samples.

Application-free, native DNA sequencing, retaining base modifications Amplification-based sequencing for low input or poor-quality DNA
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 output 3/3 2/3 2/3 2/3
Multiplexing options 24 plex, 96 plex 24 plex, 96 plex - 24 plex
Methylation included Yes Yes Yes -
Overview Optimised for output, retains base modifications, and enables control over read length. Optimised for simple and rapid library prep whilst retaining base modifications. Optimised for production of ultra-long reads (N50 ≥50 kb) and retains base modifications. Optimised for simple and rapid library preps with low input.
Buy now Buy now Buy now Buy now
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.

Recommended for whole-genome sequencing

PromethION 2 Solo and 2 Integrated

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 EPI2ME analysis pipelines are available for small genome assembly and human variant calling, amongst many others.

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


Get in touch

Talk to us

If you have any questions about our products or services, chat directly with a member of our sales team.

Book a sales call

To book a call with one of our sales team, please click below.