Installing Nextstrain

We – and our collaborators – have set up different versions of Nextstrain all around the world, on many different computer architectures. These experiences have resulted in two alternative approaches to installation, each with their own pros and cons:

1. “Local Install” which installs the augur & auspice programs themselves, so that they’re available as individual programs on the command line. We highly recommend using conda to manage environments, however there are other options. This method is detailed here.

2. “Container-based installation” We provide a container-based system using docker, which includes all of the individual components behind Nextstrain. You can then interact with this container through the nextstrain CLI (command line interface). This method is detailed here.

No matter which method you use, you’ll be able to run and modify pathogen builds on your own computer, and if you wish to, share the results through

It’s important to remember which installation method you choose, as the instructions in the tutorials will be slightly different depending on your installation approach!

Comparison of local vs container based installation

Comparison between the two methods

We’ve found that the container-based method is generally better if you want to grab one of the pathogen builds and run it with your data. If you prefer to tinker with the methods or steps, or prefer your bioinformatics tools in a more Unix-y fashion, then a local installation may be the better choice.

I’m running Nextstrain, how to I remember which installation method I used?

  • If you interact with things by running the nextstrain program, then you have a container-based installation.

  • If you enable Nextstrain through source activate nextstrain or conda activate nextstrain, and then use augur or auspice, then you have a local installation.