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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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Structural variation SNVs and phasing Gene expression Identification Splice variation Assembly Fusion transcripts Epigenetics Single cell Chromatin conformation

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Whole genome Targeted Whole transcriptome Metagenomics Short fragment mode View all Applications
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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 repository
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​ ​ ​

EPI2ME: 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

Intuitive workflows and interactive reports

A full suite of data analysis workflows for:

  • Human genomics
  • Cancer genomics
  • Assembly
  • Metagenomics
  • Single cell and transcriptomics
  • Infectious diseases 
  • Target sequencing
  • And much more…
     

The most comprehensive human genome analysis tool

 

  • A single workflow to investigate the full human genomic variation
    • Single nucleotide variants (SNVs)
    • Structural variants (SVs)
    • Methylation
    • Copy number variants (CNVs)
    • Short tandem repeat (STR) expansions
    • Phasing
  • Comprehensive reports
  • Interactive genome browser

Genome browser screenshot of a > 6 kb deletion, phased, with highly accurate SNP calling and phased modifications calling at the top.

Real-time metagenomics insights

  • From amplicon-targeted to shotgun metagenomics sequencing. 
  • Intuitive reports with powerful and interactive graphics
  • Real-time results for quick detection
  • Post-run analysis for precise identification
  • Multiple databases available
 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
Explore user-developed tools and algorithms

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