Microbial genomics
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.
Most viewed
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A successor to Sanger: accurate, full-length, and haplotype-resolved amplicon sequencing with Oxford Nanopore
In this application note, we evaluate Oxford Nanopore sequencing for amplicon analysis using matched datasets generated with both Oxford Nanopore and Sanger sequencing.
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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 whole-genome sequencing of foodborne pathogens
In this application note, we demonstrate the suitability of Oxford Nanopore sequencing as a standalone platform for foodborne pathogen whole-genome sequencing.
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GridION: one sequencer for many
Made with multiple projects and teams in mind, GridION gives you the freedom to start, stop, and scale your sequencing experiments without impacting others. Meanwhile, onboard compute keeps your real-time data optimised. Discover more.
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MinION: palm sized, world ready
Discover how the portable yet powerful MinION Mk1D sequencing device can take your insights further afield. Start generating rapid, real-time results without compromise.
Workflow overviews
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Nanopore-only microbial isolate sequencing solution (NO-MISS): flexible, rapid bacterial and fungal isolate whole-genome sequencing
This end-to-end workflow provides a rapid solution for whole-genome Oxford Nanopore sequencing of bacterial and fungal isolates.
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Streamlined identification of bacteria, archaea, and fungi with Oxford Nanopore microbial amplicon barcoding
This end-to-end workflow introduces how to sequence the full length 16S gene and ITS region with Oxford Nanopore technology.
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Rapid and complete plasmid characterisation with Oxford Nanopore sequencing
This end-to-end workflow is a rapid method for complete, high-quality whole-plasmid characterisation.
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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.
Featured resources
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Delivering the future of genomic pathogen surveillance with Oxford Nanopore sequencing
Achieve comprehensive, affordable, and real-time analysis of human and animal pathogens with nanopore sequencing.
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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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Wastewater sequencing — an early warning system for infectious disease outbreaks
Monitoring the genomic characteristics of pathogens circulating in a population can reveal important insights into the epidemiological dynamics of an outbreak. Unfortunately, sequencing every confirmed positive sample in a densely populated area is both challenging and expensive. Since viruses are s
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Testimonial: Thidathip Wongsurawat
Thidathip Wongsurawat is driven to improve patient outcomes through addressing
unmet needs. Explore why she is researching the rapid capabilities of nanopore
technology to get answers with impact.
Protocols
Microbial Amplicon Barcoding Sequencing for 16S and ITS (SQK-MAB114.24)
Step-by-step protocol for microbial 16S and ITS amplicon sequencing using the Oxford Nanopore Microbial Barcoding Kit.
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Solución de secuenciación de aislados microbianos solo con tecnología Nanopore (NO-MISS) a partir de cultivos celulares y el kit SQK-RBK114 (.24 o .96)
Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS) from cell cultures using SQK-RBK114 (.24 or .96)
Secuenciación rápida de ADN V14 - con códigos (SQK-RBK114.24 o SQK-RBK114.96)
Learn how to perform rapid genomic DNA barcoding using the Rapid Barcoding Kit V14 (SQK‑RBK114.24 / SQK‑RBK114.96). This fast, high‑yield library preparation workflow enables multiplexing of up to 96 gDNA samples with ~60‑minute prep time and compatibility with R10.4.1 flow cells.
Analysis workflows
Latest research
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Unlocking high-resolution, strain-resolved microbiome analyses | ASM Microbe 26
During this video we learn how full length Oxford Nanopore sequencing is unlocking high-resolution microbiome analyses
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Diagnostic value of nanopore-based targeted sequencing technology for subclinical tuberculosis
Publication: Diagnostic value of nanopore-based targeted sequencing technology for subclinical tuberculosis
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Understanding bacterial DNA methylation and analysis methods
In this webinar we learn how to advance microbial genomics and epigenomics research with authenticated reference resources.
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Building sustainable pathogen genomic surveillance across Africa
This webinar shares practical lessons from implementing surveillance at scale, to specimen collection and sequencing to bioinformatics and data interpretation. Explore real-world challenges, collaboration models and system-level strategies required to build resilient genomic surveillance.
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Rapid and scalable whole-genome microbial isolate sequencing
Find out how the nanopore-only microbial isolate sequencing solution provides rapid and scalable bacterial isolate sequencing.
