EPI2MELabs downloads and resources

Below are listed all resources on which EPI2MELabs is built. We aim for all components of EPI2MELabs to be open source (including this website) and available through our GitHub repository: https://github.com/epi2me-labs/tutorials.

If you find something is not available please contact support@nanoporetech.com

EPI2MELabs Launcher

The LabsLauncher is used to start, stop, and update the EPI2MELabs notebook server. We provide executables for Windows 10, macOS, and Linux.

Platform Download
Windows 10 ont-epi2melabs-installer-v1.0.8-win10.exe
macOS ont-epi2melabs-launcher-v1.0.8-macos.dmg
Ubuntu 16.04 ont-epi2melabs-launcher-1.0.8-0.xenial.deb
Ubuntu 18.04 ont-epi2melabs-launcher-1.0.8-0.bionic.deb
Ubuntu 20.04 ont-epi2melabs-launcher-1.0.8-0.focal.deb
CentOS 7 ont-epi2melabs-launcher-1.0.8-1.el7.x86_64.rpm
CentOS 8 ont-epi2melabs-launcher-1.0.8-1.el8.x86_64.rpm

The launcher is written in Python with Qt and the sourcecode is available from GitHub: https://github.com/epi2me-labs/labslauncher.

Notebook files

A listing of all available notebooks is available on the Notebook Index page.

The notebooks used within EPI2MELabs are available in their source form from the GitHub repository: https://github.com/epi2me-labs/tutorials. These are updated regularly with enhancements and fixes.

Docker containers

The docker container for the EPI2MELabs notebook server is hosted on dockerhub: https://hub.docker.com/r/ontresearch/nanolabs-notebook, with the source code for the build process on Github: https://github.com/epi2me-labs/nanolabs.

The notebook server is based on the docker-stacks

Nextflow workflows

A listing of all available notebooks is available on the Workflows Index page.

All EPI2ME Labs workflows are available open-source through our Github space; workflow projects are named with a wf-artic prefix.

The workflows can be run easily using nextflow without explicitely downloading anything from Github, for example:

nextflow run epi2me-labs/wf-artic --help

Will download our SARS-CoV-2 ARTIC sequencing workflow and display its help text. See the Workflow Quick Start for further information.

Aplanat

Aplanat is a plotting library built on top of bokeh. It allows graphs to be contructed and displayed in notebooks with minimal boiler plate. Aplanat also provides functionality to generate static HTML report documents, as used in the EPI2ME Labs Nextflow workflows.

Mapula

Mapula is an alignment statistics package designed to work on streaming data; it can be inlined in a typical samtools pipeline to calculate statistic on-the-fly.


Providing open bioinformatics resources for nanopore sequencing. Research use only. Follow us on twitter.