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Nanopore sequencing offers advantages in all areas of research. Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins.

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Data analysis: for all levels of expertise

We provide a wide range of tools to support nanopore data analysis. From end-to-end analysis workflows in EPI2ME to the latest cutting-edge tools to make the most of your sequencing runs.
Overview

Data analysis analysis for all levels of expertise

Data analysis analysis for all levels of expertise

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Who are you?

Scientist

  • Preconfigured workflows
  • No bioinformatics skills needed
  • Fully supported

EPI2ME solutions
Bioinformatician

  • Access our latest tools
  • Integrate your workflows
  • Explore community tools

Command-line tools

MinKNOW: intuitive software native to all platforms

  • Performs raw data acquisition, basecalling, and demultiplexing in real time or post run
  • Built-in methylation detection
  • Enables in silico targeted sequencing with adaptive sampling
  • Can be connected to up- and downstream tools with MinKNOW API
Get started
Intuitive software native to all platforms

End-to-end analysis workflows with EPI2ME solutions

  • Preconfigured workflows for data analysis
  • EPI2ME solutions are available as cloud or locally installed software
  • Start with sequencing data and get a detailed report
  • Choose between real-time or post-run analysis
  • Intuitive interface
Learn more

Cutting-edge analysis with the latest tools

  • Explore the latest tools and algorithms on our GitHub repositories
  • From basecallers to end-to-end workflows
  • Ready for integration into your custom pipelines
  • Command-line experience required
Learn more

Find the latest tools in the Oxford Nanopore repository

 

 

Find all our analysis workflows in the EPI2ME Labs repository

 

Join the Community

Contact support

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End-to-end workflows

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 EPI2ME solutions

Data analysis analysis for all levels of expertise

Data analysis analysis for all levels of expertise

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Data analysis for everyone: EPI2ME solutions​

  • Intuitive interface, seamless experience​
  • Run preconfigured workflows for rapid insights​
  • No bioinformatics experience required
  • Run in the cloud or locally, on your laptop or preferred machine set-up​
  • Choose between real-time or post-run analysis​
  • Keep ownership of your data from sample to answer​ ​ ​
POINT AND CLICK TOOLS

 

Download EPI2ME

EPI2ME: real-time data analysis in the cloud​ ​ ​

  • Interactive reports in the browser — shareable and printable​
  • No need for local computing capabilities or server access​
  • Install only the EPI2ME Agent software for data upload​
  • Access as a Nanopore Community member from the intuitive interface or the command line​ ​ ​

Join the Community

EPI2ME Labs: an open analysis platform

  • Standalone desktop application
  • Pre-packaged with >10 open-source workflows (Nextflow framework)
  • Compatible with Windows, macOS, and Linux
  • Install on laptop, desktop computer, cluster or cloud service, PromethION, or GridION
  • Free access from the intuitive interface or the command line
EPI2ME Labs: an open analysis platform

 

Download EPI2ME Labs

Examples of analysis workflows available

EPI2ME

  • Metagenomics classification
  • 16S classification
  • Alignment to reference
  • Clone validation
  • SARS-CoV-2 genome
  • And more

Download EPI2ME

EPI2ME Labs

  • Human variation: structural variants, SNVs and methylation
  • Bacterial genomes
  • Cas9 enrichment
  • Single cell
  • Transcriptomics
  • And more

Download EPI2ME Labs

Choose the right tool for you: in the cloud or on your computer?

 

Location

 Cloud-based Local or distributed (laptop,sequencing device, cluster, or cloud)
Analysis Real time and post run (all workflows) Post run and real time (for selected workflows)
Configurability Highly preconfigured Preconfigured with more flexible options
Resource needed Any laptop with good internet connection Computational requirements depend on dataset and analysis
Reporting Interactive, simplified, sharable reports Detailed output, shareable reports
Software EPI2ME Agent EPI2ME Labs, Docker
Bioinformatics expertise None EPI2ME, Docker
Graphical interface Yes Yes
Command-line interface Yes Yes
 

Download EPI2ME

Download EPI2ME Labs

 

Join the Community

Contact support

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End-to-end workflows

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 Command-line tools

Data analysis analysis for all levels of expertise: Command line tools

Data analysis analysis for all levels of expertise: Command line tools

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Download the latest tools from Oxford Nanopore Technologies

  • Available on the Oxford Nanopore GitHub repository
  • From the latest basecallers to newly developed research tools
  • Ready for your custom pipelines
  • Command-line experience required

Find the latest tools in the Oxford Nanopore repository

Find all our analysis workflows in the EPI2ME Labs repository

 

 

Oxford Nanopore Open Datasets

New to Oxford Nanopore data? Get started with our end-to-end analysis workflows

  • EPI2ME Labs workflows are available from the command line and from the graphical user interface
  • Implemented using Nextflow according to the nf-core schema and code is deposited in to GitHub
  • GitHub command-line execution allows:
    • Workflows to be managed automatically with finer control of parameters
    • Greater control over computational resources
    • Jobs to be run on servers, clusters, and the cloud

Access EPI2ME workflows in the cloud from the command line

  • Command-line control over cloud-based bioinformatics workflows
  • No need for local computing capabilities or server access
  • Real-time upload and analysis
  • Reports available through EPI2ME website
  • Access as a Nanopore Community member
Access EPI2ME workflows in the cloud.png

 

Learn more about EPI2ME

Explore user-developed tools and algorithms

Resource centre

Explore user-developed tools and algorithms

  • Developed by the Nanopore Community
  • Tailored to Oxford Nanopore data
  • Common tools: demultiplexing, filtering, mapping, assembling, variant calling, etc
  • Application-specific tools: bacterial genome assembly, SARS-CoV-2 monitoring, hepatitis C genome sequencing, mitochondrial DNA haplogroup classification, novel pathogen detection, transposon insertion identification, etc
  • Extended functionality: visualisation tools for methylated data, RNA methylation prediction, barcode aware adaptive sampling

 

Join the Community

Contact support

Find GitHub tools

End-to-end workflows

Resource centre

Download our software

Explore our products

Library prep

Flow cells

Devices

Data analysis