Multi Genome Alignment 2 Plugin for MultiQC

For more information about MultiQC, see https://multiqc.info

For more information about Multi Genome Alignment 2, see https://github.com/crukci-bioinformatics/MGA2

Multi Genome Alignment 2 Plugin

The plugin will add a section for Multi Genome Alignment reports to the MultiQC report. There is a plot of how reads are assigned to reference species and tabular data for each data set.

Requirements

The MGA2 plugin required Python 3.6 minimum and MultiQC version 1.9 or newer.

Installing

The easiest way to install the plugin is to add it to your Python virtual environment using pip.

python3 -m venv <path to virtual environment>
<path to virtual environment>/bin/activate
pip install git+https://github.com/crukci-bioinformatics/multiqc_mga2_plugin.git

The pip command above will also install MultiQC if it is not already present.

Installing for Development

When doing development work, the plugin will be cloned from GitHub onto your local file system. You will need to create a virtual environment and add MultiQC to it:

python3 -m venv <path to virtual environment>
<path to virtual environment>/bin/activate
pip install multiqc

Then, from the check out of the plugin, add a development installation of the plugin to the environment:

python3 setup.py develop

Running MultiQC

The MGA2 plugin will automatically be picked up by MultiQC if it is found in the environment's Python eggs. See Running MultiQC.