Metagenomics
Getting started guides
)
A guide to microbial sequencing with Oxford Nanopore
A guide to get started with sequencing microbial samples with Oxford Nanopore.
Workflow overviews
)
Performing accurate species-level bacterial identification with nanopore sequencing
This end-to-end workflow provides a rapid solution for species-level bacterial identification.
)
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.
)
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
)
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.
)
Oxford Nanopore sequencing solutions for microbiology and infectious disease research
Discover the Oxford Nanopore sequencing techniques that can achieve comprehensive microbial genome characterisation.
)
EPI2ME: data analysis for all levels of expertise
Discover EPI2ME and how it provides data analysis for all levels of expertise
Featured resources
)
Which library prep workflow is right for my experiment?
Whether you’re sequencing DNA, RNA, or cDNA, a single sample or many in multiplex, there’s an Oxford Nanopore library prep kit for you. In this masterclass, discover how to choose the right one for your workflow.
Pan-microbial pathogen detection in hours using metagenomic sequencing
In this case study, discover how the UK NHS Respiratory Metagenomics Network have developed a rapid Oxford Nanopore sequencing workflow that can detect the bacteria, viruses, fungi, and parasitic pathogens underlying respiratory infections in a matter of hours.
)
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.
)
Addressing the challenges of metagenomics with Oxford Nanopore sequencing
Explore how reads with unrestricted length are revealing unprecedented insight into microbial communities.
)
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.
Protocols
使用 SQK-RPB114.24 进行细菌、真菌和病毒病原体监测的快速宏基因组测序
本实验指南提供了一种快速的宏基因组测序方法，用于鉴定细菌、真菌和病毒性病原体。
此指南具有以下特点：
- 采用二合一流程，可将同一样品分别进行细菌/真菌与病毒/非细胞前处理；
- 提供针对呼吸道样品的宿主去除与核酸提取方法；
- 采用 RT-PCR “鸟枪法”策略；
- 包含酶切法片段化、条形码标记及 PCR 扩增步骤；
- 适用于 R10.4.1 测序芯片。
仅供研究使用
Analysis workflows
wf-amplicon
This Nextflow workflow provides a simple way to analyse Oxford Nanopore reads generated from haploid amplicons.
Latest research
Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance
Authors: Worarat Kruasuwan, Ditthawat Pathomchareansukchai, Watcharaphon Tangsawad, Natnicha Wankaew, Tantip Arigul, Perapon Nitayanon, Pattaraporn Nimsamer, Rapeephan Duangjanchot, Sopacha Arayamethakorn, Narut Chancharussin, Piroon Jenjaroenpun, Witchuda Kamolvit, Yupin Suputtamongkol, et al.
)
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
)
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
)
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
