This workshop provides an overview of phylogenetic analysis and interactive visualization using Nextstrain. Nextstrain is an open-source project to facilitate phylodynamic analysis, data integration, and visualization of large data sets of viral and bacterial pathogens. The analysis results can be visualized on your own computer or shared on the web.
Prerequisites
We hope that we can jump right in and start analyzing data and exploring the spread of disease. We therefore ask you to come to the workshop with the necessary tools installed on your computer.
We will be using basic shell commands as well, like moving and editing files, changing directories, and starting programs. There are some great resources available online to learn or refresh this basic command-line usage.
Please follow the Nextstrain CLI installation instructions on docs.nextstrain.org. These are available for all the major operating systems (Windows, Mac, Linux). On Windows you need you setup WSL2 and install Docker.
If you have trouble setting this up on your computer, please contact your IT department or computer-savvy friend.
Once you have installed the above, we recommend you configure either the docker or conda runtime for the workshop:
nextstrain setup conda
nextstrain setup docker
Check that everything works by running
nextstrain check-setup --set-default
For the rest of the tutorial, we assume that you are running all commands inside the nextstrain shell which you can start with nextstrain shell . and exit with ctrl+d or by typing exit.
Within this shell, all necessary tools are installed and ready to be used.
Important links
- nextstrain.org
- nextstrain documentation
- Example repository with zika sequences
- Time-scaled phylogenies with TreeTime
- getting miniconda
- snakemake tutorial