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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.


Data analysis analysis for all levels of expertise

Data analysis analysis for all levels of expertise


  • Preconfigured workflows
  • No bioinformatics skills needed
  • Fully supported

EPI2ME solutions

  • 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
EPI2ME solutions

Data analysis analysis for all levels of expertise

Data analysis analysis for all levels of expertise

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

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

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

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