The EPI2ME Labs Launcher is used to start, stop, and update the EPI2MELabs notebook server, our interactive environment for bioinformatics exploration and learning. We provide executables for Windows 10, macOS, and Linux.

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

Below are listed all resources on which EPI2ME Labs 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/.

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

EPI2ME Labs resources

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

The notebooks used within EPI2ME Labs 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/epi2melabs-notebook. This source code used to build this image is contained within the git repositories nanolabs and tutorials. The notebook server is based on the docker-stacks project. The EPI2ME Labs team have added bioinformatics software as well as various Jupyter extensions (including some custom additions).

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.

Other software

In the course of creating informative tutorials and tailored workflows, the Customer Workflows group at Oxford Nanopore Technologies has created several standalone packages that might be useful to other scientists in their own right.

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.

Fastcat

Fastcat is a small FASTQ utility primarily used to concatenate transparently compressed and uncompressed FASTQ files, whilst producing summaries of the input files.