Metagenomic sequencing
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'Q20+ nanopore sequencing chemistry in this single laboratory evaluation study demonstrates its potential as an alternative to [legacy technologies] for rapid and comprehensive bacterial genome analysis in outbreak investigations.'
Hoffmann et al., bioRxiv (2024)
Enhance genome assemblies
Metagenomics is the genomic analysis of multiple organisms from a single sample, revealing insight into the genetic composition of microbial communities. Any-length nanopore reads deliver enhanced genome assemblies, accurate identification of closely related species, and resolve mobile genetic elements from metagenomic samples. With nanopore sequencing, real-time data streaming unlocks immediate access to results, such as species identification, relative abundance, and antimicrobial resistance (AMR) analysis. Furthermore, combining long reads with targeted approaches enables sequencing of informative genes, such as 16S ribosomal RNA (rRNA) in their entirety, improving resolution of identification.
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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.
Addressing the challenges of metagenomics with Oxford Nanopore sequencing
Explore how nanopore sequencing is addressing the challenges of metagenomics to obtain complete or nearly complete genome sequences from uncultured microorganisms — providing important means to study their biology, ecology, and evolution.
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Recommended device for metagenomic sequencing
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PromethION 2 devices
Offering flexible, affordable, high-output nanopore devices for every lab in a compact, accessible form, the PromethION 2 Solo and PromethION 2 Integrated devices are ideal for obtaining complete circular genomes from complex metagenomic samples in real time.
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)
- 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
- 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)
- 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
- 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
