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Getting started guides

Preview of the microbial getting sequencing getting started guideGetting started guide

A guide to microbial sequencing with Oxford Nanopore

A guide to get started with sequencing microbial samples with Oxford Nanopore.


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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.
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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.

Workflow overviews

Preview of the NO-MISS workflow overviewWorkflow overview

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.
Microbiology MetagenomicsWorkflow overview

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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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.
From_full-length_16S_to_high-resolution_metagenomics_choosing_the_right_microbial_community_workflowEvent video

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
Which_library_prep_workflow_is_right_for_my_experimentEvent video

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. In this masterclass, discover: • The range of Oxford Nanopore library prep solutions av

Protocols

Rapid sequencing DNA - PCR Barcoding Kit 24 V14 (SQK-RPB114.24)

This protocol: Uses genomic DNA Has a low input requirement Has a method involving tagmentation, barcoding and PCR amplification Allows multiplexing of 1–24 samples Is compatible with R10.4.1 flow cells For Research Use Only
SQK-RBK110.96 gDNA workflow v1

Rapid sequencing DNA V14 - barcoding (SQK-RBK114.24 or 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.

Ligation sequencing DNA V14 (SQK-LSK114)

This protocol describes how to carry out sequencing of a DNA sample using the Ligation Sequencing Kit V14 (SQK-LSK114). It is recommended that a Lambda control experiment is completed first to become familiar with the technology.

Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24)

This protocol describes how to carry out native barcoding of genomic DNA (gDNA) using the Native Barcoding Kit 24 V14 (SQK-NBD114.24).

Ligation sequencing gDNA - Native Barcoding Kit 96 V14 (SQK-NBD114.96)

This document describes the barcoding of native genomic DNA libraries. For Research Use Only

Analysis workflows

wf-metagenomics

This workflow can be used for the taxonomic classification of metagenomic sequencing data.

wf-bacterial-genomes

This workflow is primarily used to assemble genomes from bacterial reads and provide information on features of interest within those assemblies through annotations.

wf-amplicon

This Nextflow workflow provides a simple way to analyse Oxford Nanopore reads generated from haploid amplicons.

wf-alignment

This workflow provides an easy way to align Oxford Nanopore reads and gather mapping stats either locally for small amounts of data or at scale in a distributed environment such as a cluster or the cloud.

wf-16s

This workflow can be used for taxonomic classification of single reads from amplicon-targeted sequencing.

Latest research

Aaron Pomerantz Publication Real-time DNA barcoding in a rainforest using nanopore sequencing opportunities for rapid biodiversity assessments and local capacity buildingPublication

​Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa

​Publication: Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa
European hare sitting in a field of flowersPublication

Barcode 100K specimens: in a single nanopore run

Publication: Barcode 100K specimens: in a single nanopore run
Bacterial community- metagenomicsPublication

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Strand of DNA with bases highlighted in yellowPublication

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Publications: Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Pallas CatPublication

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

Getting started

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