Sequencing software EPI2ME

data analysisreal-time

Product overview
Oxford Nanopore provides software and tools for nanopore sequencing data analysis, combining EPI2ME preconfigured workflows and the MinKNOW operating environment. Solutions support real-time analysis and deployment on laptops, workstations, clusters, cloud environments and Oxford Nanopore devices to meet research and clinical laboratory needs.

Preconfigured analysis workflows with EPI2ME

• Accessible via an intuitive desktop application or command-line interface
• Preconfigured workflows available for multiple sequencing applications
• Deploy and run analyses on laptop, cluster, cloud or ONT devices
• Obtain results during sequencing with real-time workflows
• Create and share custom workflows through the EPI2ME application

For scientists

• User-focused interfaces for routine data inspection
• Structured reports for rapid interpretation of results
• Many workflows operate without specialised bioinformatics expertise
• Data ownership retained from sample to result

For bioinformaticians

• Access basecallers and analysis tools via the Oxford Nanopore GitHub repositories
• Obtain EPI2ME workflow definitions from GitHub or integrate custom code
• Command-line support enables advanced and automated integrations

MinKNOW

• Operating software for Oxford Nanopore sequencing devices
• Manages raw data acquisition and basecalling
• Includes integrated methylation detection where applicable
• Supports in silico targeted sequencing via adaptive sampling
• Provides an API for connections to upstream and downstream tools

Datasets and compatible solutions

• Open datasets are provided to support method development and benchmarking
• Oxford Nanopore collaborates with tertiary analysis partners for end-to-end interpretation solutions
• Online training and masterclasses available to support user adoption

Technical specifications

• EPI2ME: preconfigured, real-time workflows; desktop application and command-line interfaces
• Deployment: supports laptop, workstation, cluster, cloud, and ONT devices
• Real-time analysis: access to intermediate and final results during sequencing
• Customization: build, export and share custom workflows via EPI2ME
• MinKNOW: data acquisition, basecalling, methylation detection, adaptive sampling, MinKNOW API for integrations
• Tools and basecallers: maintained and accessible via Oxford Nanopore repositories for advanced users
• Target audiences: laboratory scientists (minimal bioinformatics required for many workflows) and bioinformaticians (command-line and integration support)