Applications Research areas
Environmental genomics
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
- Sequence in low resource environments with limited access to cold storage using the Field Sequencing Kit
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.
Streamlined workflows
- Sample prep in as little as 10 minutes, including multiplexing
- Whole genome, metagenomic, targeted, direct RNA, and cDNA sequencing approaches
- Eliminate amplification bias and GC bias, and detect base modifications alongside nucleotide sequence with amplification-free protocols
- Automate sample prep using the portable VolTRAX device
Laborious workflows
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.
White paper
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.
Get more environmental sequencing content, including eDNA, metabarcoding, and metagenomics publications, posters, and videos, in our Resource centre, or visit our Portable sequencing page.
ORG.one
Supporting rapid sequencing of critically endangered species, anywhere, by anyone
ORG.one is a pilot-stage project designed to support faster, more localised sequencing of critically endangered species, by enabling biologists to rapidly sequence those species close to the sample’s origin, using the latest ultra-long read approaches.
Data-rich, de novo whole-genome assemblies will be enabled through the provision of consumable support that can be used with Oxford Nanopore sequencers, on the condition that the data generated will be openly shared with the scientific community.
ORG.one supports the sequencing of species from the IUCN Red List, specifically the critically endangered and extinct in the wild categories (more than 8000 species)
Case study
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)
Discover more about the benefits of nanopore sequencing for species identification, metagenomics, and whole genome assembly in our applications pages.
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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.
Recommended for environmental genomics
MinION Mk1C
A powerful, portable, and affordable all-in-one sequencing and analysis device. Perform real-time sequencing at sample source for the fastest access to results. Ideal for in-field or lab-based analysis of eDNA, metabarcoding, and metagenomics.
VolTRAX
Portable, USB-powered, automated sample extraction and library preparation — use predefined or custom protocols.
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Flongle
Adapting MinION and GridION to run our lowest cost flow cells — ideal for low throughput metabarcoding projects.
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MinION
All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device — available from just $1,000, including sequencing reagents.
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GridION
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.
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PromethION 2 & 2 Solo
Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing - ideal for smaller sample number whole-genome and transcriptome projects. Available to preorder now.
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PromethION 24
Offering 24 independent, high-capacity flow cells and powerful, integrated compute, PromethION 24 delivers flexible access to terabases of sequencing data — ideal for high-throughput labs and highly multiplexed samples.
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PromethION 48
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.
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