Applications Research areas
Portable, affordable nanopore sequencing technology delivers unique opportunities for environmental research and has been used extensively to analyse environmental DNA (eDNA) and microbiome samples to support biodiversity assessment, ecosystem biomonitoring, pathogen identification, and animal conservation. Long nanopore sequencing reads provide enhanced species identification, while real-time data analysis delivers immediate access to results, whether in the field or in the lab.
Entirely off-grid and solar-powered eDNA sequencing
Off-grid sequencing reduced the time from sample-to-data to under 5 hours… Gowers, G.F. et al. Genes 10:11 (2019)
Oxford Nanopore sequencing
Traditional short-read technologies
Sequence at sample source or lab
- Powerful, portable devices — starting at just $1,000, including sequencing reagents
- Get faster access to results — no more sample shipping delays
- Minimise potential for sample degradation — reveal the true biology
Constrained to the lab
Traditional sequencing technologies are typically bulky, cumbersome to ship, and require substantial site infrastructure, making them difficult to deploy in mobile settings or remote locations — where much of the world’s biodiversity is located.
Real-time data streaming
- Analyse data as it is generated for rapid insights
- Stop sequencing when sufficient data obtained — wash and reuse flow cell
- Use intuitive EPI2ME workflows for real-time microbiome analysis
Fixed run time with bulk data delivery
Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.
Unrestricted read length (>4 Mb achieved)
- Get enhanced phylogenetic and taxonomic resolution through metabarcoding with full-length reads of informative loci (e.g. entire 16S and CO1 genes)
- Assemble complete genomes and plasmids from metagenomic samples — resolving similar species and complex genomic regions
Read length typically 50–300 bp
Short sequencing reads may not span complex genomic regions, reducing the contiguity of metagenome assemblies. Metabarcoding of specific regions of interest with short reads has been reported to provide limited phylogenetic resolution.
- Sample prep in as little as 10 minutes, including multiplexing
- Whole genome, metagenomic, targeted, direct RNA, and cDNA sequencing approaches
- Eliminate amplification bias and detect base modifications alongside nucleotide sequence with amplification-free protocols
- Automate sample prep using the portable VolTRAX device
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency. Base modifications (e.g. methylation) are not detected as standard, with extra preparation steps and additional sequencing runs required.
Addressing the challenges of metagenomics
Microbial communities can have a profound effect on their environment, for example breaking down pollutants or generating useful by-products. In the same manner, environmental pressures, such as climate change, can impact the constitution of microbial communities. As a result, metagenomic analysis, which interrogates the genetic material of all microorganisms in a given community, not only provides significant insights into the structure and function of microbial communities but can also act as an environmental monitoring system. This White paper explores the challenges of metagenomics, with real-world examples of how they are now being addressed through the use of nanopore sequencing technology.
In-field biodiversity monitoring using the portable MinION
The analysis of eDNA and environmental metabarcoding can provide powerful insights into biodiversity, conservation, contamination, invasive species, and potentially harmful pathogens. In this paper, Krehenwinkel et al. provide a comprehensive review of how portable, real-time nanopore sequencing is being deployed to support biomonitoring and biodiversity assessment in a range of environments.
'it is not surprising that past years have seen an increased application of nanopore sequencing for biodiversity explorations, with researchers from around the world capitalizing on its simplicity, accessibility, cost effectiveness and mobility'Krehenwinkel et al. Genes 10:11(2019)
Scalable sequencing for environmental genomics
From portable yet powerful Flongle and MinION devices to the flexible, high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific environmental sample sequencing requirements.
Portable, USB-powered, automated sample extraction and library preparation — use predefined or custom protocols.View product
Adapting MinION and GridION to run our lowest cost flow cells — ideal for low throughput metabarcoding projects.View product
All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device — available from just $1,000, including sequencing reagents.View product
A compact benchtop device offering powerful integrated compute with on-demand access to 5 independent MinION Flow Cells — run multiple eDNA, metabarcoding, or metagenomics projects on a single device.View product
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of sequencing data — ideal for high-throughput labs and population-scale projects.View product
Our most powerful platform, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large sample numbers.View product