Setup and installation
The following steps will prepare you to run complete analyses of SARS-CoV-2 data by installing required software and running a simple example workflow.
Table of Contents
Register for a GISAID account
Some tutorials rely on data downloaded from GISAID. If you do not already have one, register for a GISAID account now. Registration may take a few days.
Install Nextstrain components
Follow instructions to install Nextstrain components.
Note
If using the native runtime, install these additional packages necessary to run the ncov workflow. Make sure to activate the correct conda environment.
mamba install -c conda-forge -c bioconda \
epiweeks nextclade nextalign pangolin pangolearn
Download the ncov workflow
Use Git to download a copy of the ncov repository containing the workflow and this tutorial.
git clone https://github.com/nextstrain/ncov.git