Targeted sequencing
Getting started guides
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A guide to targeted sequencing with Oxford Nanopore
This guide provides an introduction to performing targeted nanopore sequencing.
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A guide to human genomics with Oxford Nanopore
This guide introduces how to sequence human genomes with Oxford Nanopore, from the construction of new, highly complete reference assemblies to the comprehensive identification of variants.
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A guide to investigating methylation in the human genome
This guide provides an introduction to the direct sequencing of DNA methylation in human genomes.
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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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 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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Real-time enrichment of a comprehensive pharmacogenomic panel with Oxford Nanopore sequencing
This end-to-end workflow introduces how to enrich a comprehensive panel of PGx targets with real-time targeted Oxford Nanopore sequencing.
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Rapid and scalable full-length amplicon validation with Oxford Nanopore sequencing
This end-to-end workflow introduces how to validate full-length amplicons with Oxford Nanopore sequencing.
Most viewed
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Library preparation using epMotion and Oxford Nanopore Technologies Native Barcoding Kit 96 V14
In this application note, discover an automated solution for preparing up to 96 sequencing libraries with the Oxford Nanopore Native Barcoding Kit 96 V14 on the Eppendorf epMotion systems.
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Library preparation using the Ligation Sequencing Kit XL V14 from Oxford Nanopore Technologies on epMotion
In this application note, explore how the Oxford Nanopore Ligation Sequencing Kit XL V14 can be seamlessly automated on the Eppendorf epMotion systems.
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cDNA-PCR Sequencing Kits
In this flyer, discover how you can sequence full-length transcripts and annotate the transcriptome with confidence.
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Direct RNA Sequencing Kits
In this flyer, discover how you can sequence RNA in its native form. Plus, learn how the new Direct RNA Barcoding Kit unlocks multiplexed sequencing of up to 24 samples in a single run.
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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.
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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Accelerating cancer research through comprehensive genomic analysis
Unlock previously hidden variation with nanopore sequencing and characterise cancer at unprecedented resolution.
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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
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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
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Plasmid sequencing from DNA using SQK-RBK114 (.24 or .96)
This protocol describes how to carry out rapid barcoding of plasmid DNA using the Rapid Barcoding Kit 24 or 96 V14 (SQK-RBK114.24 or SQK-RBK114.96) to sequence up to 96 plasmid samples.
Amplicon sequencing from DNA using SQK-RBK114 (.24 or .96)
This is the fastest and simplest protocol to sequence amplicon DNA.
For Research Use Only
Document version: RAA_9198_v114_revM_17Oct2025
Analysis workflows
Latest research
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Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections
Authors: Qingmei Deng, Yanzhe Liu, Jian Zhang, Hongshan Zhang, Yiyong Zhang, Meng Wang, Min Jia, Dushan Ding, Yuqin Fang, Yunfei Wang, Hongcang Gu, Hongzhi Wang
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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
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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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Sensitive long-read amplicon sequence variant recovery with savont
Publication: Sensitive long-read amplicon sequence variant recovery with savont
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Performance evaluation of a PCR/nanopore assay for carrier screening for cystic fibrosis, spinal muscular atrophy, and fragile X syndrome
Publication: Performance evaluation of a PCR/nanopore assay for carrier screening for cystic fibrosis, spinal muscular atrophy, and fragile X syndrome
