EPI2ME Labs Quick Start

December 05, 2022
2 min read

EPI2ME Labs facilitates routine bioinformatics analyses by allowing users to run Nextflow) workflows in a desktop application with an easy-to-use graphical interface. The app has been designed with ease of installation in mind in order to make sequencing data analysis as accessible as possible. Find installers for all major operating systems on our Downloads page and click here for guidance on how to install.


Every time EPI2ME Labs is started, it checks if all dependencies required for running workflows are available. If one or more are missing, it will show a panel letting you know that some additional setup is required. Click on the panel and the app will guide you through installing whatever dependency is still lacking. You can also refer to the Installation page for extra information.

Setup required
'Setup required' panel when dependencies are missing

Installing workflows

Scroll down on the landing page to find the workflows available. Click on the card of one of the workflows you are interested in and confirm the download by clicking “Install workflow”. The workflow will then be downloaded and saved on your machine for later use.

Installing workflows
Workflows available for installing within the app

Importing workflows

You can also import your own (or community-developed) workflows as long as they adhere to some design principles. Have a look at this post to see if the workflow in question needs tweaking before it can be imported. To import a workflow, navigate to the Workflows tab and click on the “Import workflow” button.

Running a workflow

Once you have installed one or more workflows, head to the Workflows tab and click on a workflow you would like to run. From the next view you can launch the workflow (with your own data or a demo dataset) or go to results of previous runs. You can also open the folder where the workflow files are stored or switch to a different version.

Workflow page
Before launching a workflow with your own data, you can also try it out with a demo dataset

In order to run the workflow, click on the big button to open the launch wizard. Fill out the form (required parameter groups are marked with a red “X” which will turn to a green tick when filled out correctly) and press the “Launch workflow” button.

Workflow launch wizard
Parameters are organised in collapsible groups in the workflow launch wizard

As soon as the run has started, the app will take you to a different view from where you can interrupt the workflow or view the logs.

Running workflow logs
You can view the Nextflow logs while the workflow is running

You can go back to the workflow’s main page and then click “Workflow history” to see the run we just started.

Workflow history
Current and previous workflow runs are available in the workflow history

Once the workflow finishes, we can have a look at the report.

Workflow report
Every workflow produces a report upon completing a run


Table Of Contents

Installing workflows
Importing workflows
Running a workflow

Quick Links

TutorialsWorkflowsOpen DataContact

Social Media

© 2020 - 2023 Oxford Nanopore Technologies plc. All rights reserved. Registered Office: Gosling Building, Edmund Halley Road, Oxford Science Park, OX4 4DQ, UK | Registered No. 05386273 | VAT No 336942382. Oxford Nanopore Technologies, the Wheel icon, EPI2ME, Flongle, GridION, Metrichor, MinION, MinIT, MinKNOW, Plongle, PromethION, SmidgION, Ubik and VolTRAX are registered trademarks of Oxford Nanopore Technologies plc in various countries. Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.