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Nextstrain build for Sars-Cov-2

This repository provides the data and scripts for Sars-CoV-2 Nextstrain build and visualisation.

Install

To view Sars-CoV-2 data visualisations in your computer you need to install auspice.

To get auspice up and running follow these steps:

• If you don't have miniconda already in your computer, install miniconda3, following instructions on miniconda website at https://docs.conda.io/en/latest/miniconda.html, otherwise proceed to next step.

• In terminal, create conda environment.

conda create -n next2 python=3

• Enter to conda environment.

conda activate next2

• Install nodejs into conda environment.

conda install -c conda-forge nodejs=10

• Install auspice server.

npm install --global auspice

Now you should have software environment ready.

• Next, you need data, to get this dataset, (fork and) clone this repository to your computer.

For example, let's clone this repo to Downloads folder in your home directory, and then enter this cloned folder.

For the next step (Running) you need to be inside sars-cov2-est folder.

cd Downloads
git clone https://github.com/avilab/sars-cov2-est.git
cd sars-cov2-est

Running

To run visualisations, either type and enter:

npm start

OR

Run auspice on your dataset directly:

auspice view --datasetDir auspice

Now, if everything goes as expected, you should see instructions in your terminal that direct you to web browser where you find Sars-CoV-2 dataset and start exploring.

Build

To rebuild this dataset, in case you append new sequences, you need also install Augur and dependencies as described in https://nextstrain.org/docs/getting-started/local-installation#install-augur--auspice-with-conda-recommended.