PATH pipelines

A collection of bioinformatic pipelines for analysis of SARS-COV-2 WGS in Zambia with an emphasis on ONT outputs.

Getting started

In order to get started you will have to install git and conda.

1. Go here and follow the installation instructions appropriate for your operating system to install git. Or install your favourite git GUI.
2. Go here to download conda. I would recommend downloading the Miniconda version that is appropriate for your operating system. Choose the version that uses Python 3.

Once you have completed steps 1. and 2., you should be able to clone this repository and install the conda environment. Using terminal, navigate to a folder where you keep your bioinformatics projects. Then type:

git clone https://github.com/danieljbridges/Path_nCoV.git
cd Path_nCoV
conda env create

Now you will have download all the code and installed all the dependencies required for the workflows.