Single nucleotide variants (SNVs) and phasing
Highly accurate haplotype-resolved assemblies enabled us to access previously inaccessible regions, highlighting new forms of genetic variation and providing new insights into mutational processes
Liao, W.W. et al. Nature (2023)
Phase SNVs and resolve compound heterozygosity using long sequencing reads
Perform real-time analysis with high precision and recall
Scale to your requirements with a range of nanopore sequencing platforms
Simplify haplotype phasing
Single nucleotide variants (SNVs) have been widely studied for their associations with phenotypic variation and disease; they are also used to phase haplotypes. However, the use of traditional sequencing technology requires PCR, limiting SNV detection to regions amenable to amplification, and short reads make phasing challenging to resolve. With nanopore technology, long, PCR-free sequencing reads are generated, revealing single-nucleotide polymorphisms (SNPs) in regions inaccessible to other technologies, and phasing is greatly simplified.
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Calling and phasing single nucleotide variants in the human genome
From sample to answer, this workflow takes you step by step through our best-practice recommendations for accurately phasing variants across the human genome.
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Telomere sequencing and phasing
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PromethION 24
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of ultra-rich sequencing data — ideal for comprehensive variant identification across large numbers of samples.
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Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
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Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
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Compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells.
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The only portable, real-time devices for DNA and RNA sequencing, giving complete control and creativity over when, where, and how often you sequence, regardless of application.
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Adapting MinION and GridION devices to enable direct, real-time DNA sequencing, or cDNA sequencing, on smaller, single-use flow cells.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (50–300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
