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.
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.
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
One platform — comprehensive analysis
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 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; 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 |
| Buy now | Buy now | Buy now | Buy now | |
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.
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.
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.
With 48 independently addressable, high-yield flow cells and powerful, integrated compute, PromethION 48 delivers highly accurate genome assemblies at population scale.
Flexible, population-scale sequencing using up to 24 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large sample numbers.
Flexible, high-yield nanopore sequencing for every lab. The PromethION 2 devices are designed to be compact and accessible, utilising two PromethION Flow Cells that can generate hundreds of gigabases of data each.
From genome assembly to gene expression, run multiple experiments on-demand using five independent MinION or Flongle Flow Cells.
Access the benefits of nanopore technology from just $1,000 — suitable for whole-genome sequencing of microbial and other small genomes.
Adapting MinION and GridION for smaller, routine tests and analyses. Suitable for analysis of microbial cultures, low plex targeted sequencing, RNA isoform analysis, and quality control applications.
Analysis techniques for whole-genome sequencing
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
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