Assembly
The ability to simultaneously capture genomic and epigenomic data with Oxford Nanopore has provided unprecedented insights into the genetic and epigenetic landscape of the Przewalski’s horse.
Flack, N. et al., G3: Genes, Genomes, Genet. (2024)
Generate highly contiguous de novo and T2T assemblies with ultra-long nanopore-only reads
Explore epigenetic modifications and eliminate bias through direct sequencing of native DNA
Scale your sequencing to your needs — from small microbial genomes to large plant genomes
Generate highly contiguous genome assemblies
High-quality genome assemblies are crucial for their use as reliable reference sequences. However, the short reads produced by legacy sequencing technologies lead to highly fragmented, incomplete assemblies. Short reads cannot span important genomic regions, such as repeats and structural variants (SVs), resulting in incorrect assembly. In contrast, nanopore technology can deliver long and ultra-long sequencing reads (current record >4 Mb), that can span complex and repeat-rich genomic regions, enabling the generation of highly contiguous reference-quality genome assemblies.
Using nanopore sequencing alone, it is now possible to generate complete telomere-to-telomere (T2T) assemblies, including highly accurate Q50 whole human genomes. Register your interest in our T2T product bundle.
)
Featured content
)
Human genome assembly
Gain comprehensive insights into human genetic variation with this simple human genome assembly workflow, starting from a blood research sample, to generate a fully characterised, complete genome assembly.
)
New insights into large genomes
Thousands of complete genomes have been sequenced, but the majority of sequenced genome assemblies contain numerous gaps. Find out how nanopore sequencing is being utilised to generate more accurate and complete large genome assemblies.
Related content
)
)
)
)
PromethION 24 and 48
Combine up to 24 or 48 independently addressable flow cells with flexible, large-scale, direct DNA and RNA sequencing devices for on-demand access to terabases of data — ideal for high-throughput sequencing and assembly of large and complex genomes.
)
Adapting MinION and GridION devices to enable direct, real-time DNA sequencing, or cDNA sequencing, on smaller, single-use flow cells.
)
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.
)
A compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells.
)
Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (<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 and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- 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
