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.

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.


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