Metagenomics
Getting started guides
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A guide to microbial sequencing with Oxford Nanopore
A guide to get started with sequencing microbial samples with Oxford Nanopore.
Workflow overviews
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Performing accurate species-level bacterial identification with nanopore sequencing
This end-to-end workflow provides a rapid solution for species-level bacterial identification.
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Rapid viral sequencing for genomic surveillance of mpox using metagenomic or targeted approaches
This end-to-end workflow provides guidance for both metagenomic and targeted viral genome sequencing to deliver rapid and actionable results.
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Rapid identification of respiratory pathogens with Oxford Nanopore metagenomics
This end-to-end workflow introduces how to rapidly identify bacterial, fungal, and viral pathogens from respiratory research samples using metagenomic Oxford Nanopore sequencing on a MinION or GridION.
Most viewed
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Oxford Nanopore sequencing provides superior metagenome-assembled genome recovery and strain-level resolution from a complex microbiome
In this application note, we demonstrate the
capabilities of Oxford Nanopore metagenomics by
sequencing and analysing the well-characterised
ZymoBIOMICS Fecal Reference.
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Oxford Nanopore sequencing solutions for microbiology and infectious disease research
Discover the Oxford Nanopore sequencing techniques that can achieve comprehensive microbial genome characterisation.
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EPI2ME: data analysis for all levels of expertise
Discover EPI2ME and how it provides data analysis for all levels of expertise
Featured resources
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Genomics for a changing planet: sequencing the living world
Discover how a global community of researchers are harnessing Oxford Nanopore sequencing to study the far-reaching impacts of climate change, revealing deep insights across environmental research, agriculture, and pathogen surveillance.
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Addressing the challenges of metagenomics with Oxford Nanopore sequencing
Explore how reads with unrestricted length are revealing unprecedented insight into microbial communities.
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High-quality bacterial genomes without the complexity
In this case study, researchers show that near-complete bacterial genomes can be assembled using nanopore sequencing alone.
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From full-length 16S to high-resolution metagenomics: how do I choose the right microbial community workflow for my experiment?
In this masterclass, find the right microbial community sequencing workflow to meet your experimental goals. We’ll cover microbial identification from full-length 16S/ITS sequencing through to comprehensive metagenomic assembly. In this masterclass, discover: • How Oxford Nanopore sequencing deliver
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How do I analyse my Oxford Nanopore sequencing data without specialist training?
In this beginner-friendly masterclass, discover how to analyse your Oxford Nanopore sequencing data. Find out how basecalling works, the common file formats you’ll encounter, and how to use MinKNOW to set up and monitor your sequencing run. Then, discover how to analyse your data with EPI2ME — no pr
Protocols
Rapid metagenomic sequencing for surveillance of bacterial, fungal and viral pathogens using SQK-RPB114.24
This is a rapid method to perform metagenomic sequencing for identification of bacterial, fungal and viral pathogens.
For Research Use Only
Analysis workflows
wf-amplicon
This Nextflow workflow provides a simple way to analyse Oxford Nanopore reads generated from haploid amplicons.
Latest research
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From culture to clarity in four hours: accelerating clinical management of bloodstream infections using metagenomics
Authors: Jawad Ali, Anurag Basavaraj Bellankimath, Silje Therese Opgård, Emil Varman Manivannan,
Gunnar Skov Simonsen, Rafi Ahmad
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The planktonic microbiome of the Great Barrier Reef
Authors: Steven Robbins, Marko Terzin, Katherine Dougan, Julian Zaugg, Sara C. Bell, Patrick W. Laffy, J. Pamela Engelberts, Kim-Anh Lê Cao, Renee K. Gruber, Nicole S. Webster, David G. Bourne, Philip Hugenholtz, Yun Kit Yeoh
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
Authors: Adela Alcolea-Medina, Luke B Snell, Gul Humayun, Noor Al-Yaakoubi, Daniel Ward, Christopher Alder, Vishwa Patel, Fredrik Vivian, Christopher I S Meadows, Duncan Wyncoll, Richard Paul, Nick Barratt, Rahul Batra, Jonathan Edgeworth, Gaia Nebbia, James Whitehorn
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Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis
Authors: Kumeren N Govender, Teresa L Street, Nicholas D Sanderson, Laura Leach, Marcus Morgan, David W Eyre
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Performance and practicality of 16S nanopore sequencing for routine bacterial identification in clinical samples
Authors: A.U. Geers, C. Bütikofer, M. A. Terrazos Miani, S. Droz, A. Zihler Berner, I. Lendenmann, C. Hirzel, P.M. Keller, F. Suter-Riniker, S. Neuenschwander, C. Casanova, A. Ramette
