nCoV-2019 novel coronavirus bioinformatics environment setup

This document is part of the nCoV-2019 Nanopore sequencing protocol package:

http://artic.network/ncov-2019

Related documents:

nCoV-2019 Nanopore bioinformatics protocol:

http://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html

Funded by the Wellcome Trust

Collaborators Award 206298/Z/17/Z --- ARTIC network

Preparation

Equipment required:

Laptop requirements for MinION:

Intel i7 or Xeon processor

16GB RAM

1TB SSD hard drive

USB 3

Full Oxford Nanopore Technologies lab and computing requirements are here.

Software Setup

These protocols instructions assume a 64-bit UNIX, Linux or similar environment. This could be Mac OS X (Yosemite or later), Linux (e.g., Ubuntu 16 or later), or Windows 10 Subsystem for Linux. It assumes familiarity with a UNIX-like bash command-line.

The steps in this document should be done and tested prior to sequencing, particularly if this will be done in an environment without internet access or where this is slow or unreliable. Once this is done, the bioinformatics and phylogenetics protocols can be performed largely off-line.

Conda

Software will be installed using Conda – a cross-platform package and dependency installer.

For Conda installation instructions for your operating system go to: https://conda.io/docs/user-guide/install/. We suggest installing the Miniconda version which is relatively small and quick to install.

NOTE: Install the 64-bit Python 3.6 version of Miniconda

Installing ARTIC nCoV-2019 specific data and software

Install the ARTIC nCoV-2019 data and software repository:

git clone --recursive https://github.com/artic-network/artic-ncov2019.git

Create a custom Conda environment for running software. This may take some time as it will install the required packages and all their dependencies.

conda env create -f artic-ncov2019/environment.yml

Although not strictly necessary this will prevent any conflicts with other similar software installed and can be readily removed. You can use this command to activate the environment:

conda activate artic-ncov2019

and then deactivate it again using this:

conda deactivate

The artic environment can be removed using this:

conda remove --name artic-ncov2019 --all

Installing Oxford Nanopore MinKNOW software

The software for running the MinION and basecalling can be downloaded from the Oxford Nanopore Technologies Community site. Log in to find the Software Downloads button. Download MinKNOW (currently v19.12.2) appropriate to the system being used. Follow the Installation guide for each package.

MinKNOW is a graphical user-interface programme that will be installed in the application area of the system.