Infectious disease
This method will save time in obtaining high-quality complete genomes of bacteria for antimicrobial resistance surveillance, and is likely to become a valuable tool for monitoring the transmission of plasmid-borne drug resistance genes
Zhao et al. Front. Microbiol. (2023)
Immediate access to actionable results with real-time data — including pathogen identification and AMR profiling
Rapidly characterise and identify pathogens using fast and flexible end-to-end workflows in the lab or field
Resolve complete bacterial and viral genomes and mobile genetic elements with long nanopore reads
Rapid access to results
Offering comprehensive, real-time insights into the genomics of infectious diseases — from pathogen identification and antimicrobial resistance (AMR) profiling to the assembly of high-quality genomes and variant identification — nanopore sequencing delivers immediate access to the critical genomic epidemiology data required to effectively control infectious disease outbreaks. Sequence in the lab or at sample source at a scale that suits your needs, with powerful portable and high-throughput nanopore sequencing devices.
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Pathogen metagenomics
Metagenomic sequencing is a key technique for the identification of potential pathogens. This end-to-end workflow overview introduces how to rapidly identify bacterial, fungal, and viral pathogens from respiratory research samples using metagenomic sequencing.
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Delivering the future of genomic pathogen surveillance
Find out how nanopore sequencing overcomes the limitations of legacy genomic analysis technologies to deliver rapid, affordable, and informative results for a range of pathogen outbreaks, including SARS-CoV-2, Zika, Ebola, and many more — improving surveillance of infectious diseases.
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AmPORE-TB
AmPORE-TB is a research workflow that delivers rapid characterisation of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis, species identification, and lineage identification in a single assay, directly from sputum samples.
Combining fast library preparation with on-demand nanopore sequencing and hands-off, comprehensive analysis onboard the GridION AmPORE-TB device, the AmPORE-TB workflow can take as little as six hours for same-day results.
The GridION AmPORE-TB device, installed with the AmPORE-TB data analysis software, will be distributed by bioMérieux (Q-GRD-MK1-ATB).
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GridION
A compact benchtop device designed to run and analyse up to five MinION Flow Cells. Run multiple experiments on a single device, on-demand — ideal for rapid and scalable analysis of pathogen samples and tracking novel variants.
EPI2ME wf-flu
This workflow performs filtering, genetic variant calling, and sequence alignment to the CDC influenza reference. The analysis can be run using a fully automated, point-and-click user interface or via the command line.
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Bring streamlined genomics into your lab with the sample-to-answer automated sequencing solution. For users seeking a hands-free, simplified genomic workflow that goes from sample to data analysis.
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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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Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
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A flexible, large-scale, direct DNA and RNA sequencing device — delivering on-demand access to terabases of data.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 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 short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- 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)
- 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
- 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
- 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
- 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, and targeted (including 16S barcoding) 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
