Quickstart

This guide uses the Nextstrain command-line interface (CLI) to help you get started running and viewing the pathogen builds you see on nextstrain.org. It assumes you are comfortable using the command line and installing software on your computer. If you need help when following this guide, please reach out by emailing us, or create a post at discussion.nextstrain.org.

When you’re done following this guide, you will have built a local version of our example Zika analysis and viewed the results on your computer. You’ll have a basic understanding of how to run builds for other pathogens and a foundation for understanding the Nextstrain ecosystem in more depth.

Setup

Install Nextstrain including the Nextstrain CLI. These instructions will install all of the software you need to complete this quickstart and other tutorials.

If you’ve already installed Nextstrain, activate the Nextstrain environment.

conda activate nextstrain

Download the Nextstrain Zika tutorial repository

We store our pathogen analyses in a version control repository, so we can easily track changes over time. Download the example Zika pathogen repository you’re going to build.

$ git clone https://github.com/nextstrain/zika-tutorial
Cloning into 'zika-tutorial'...
[...more output...]

When it’s done, you’ll have a new directory called zika-tutorial/.

Run the build

Nextstrain builds use the Augur bioinformatics toolkit to subsample data, align sequences, build a phylogeny, estimate phylogeographic patterns, and save the results in a format suitable for visualization with Auspice.

Run the build with the Nextstrain CLI.

$ nextstrain build --cpus 1 zika-tutorial/
Building DAG of jobs...
[...a lot of output...]

This should take just a few minutes to complete. To save time, this tutorial build uses an example dataset which is much smaller than our live Zika analysis.

Output files will be in the directories zika-tutorial/data/, zika-tutorial/results/ and zika-tutorial/auspice/.

Visualize build results

View the build results using Nextstrain’s visualizations.

$ nextstrain view zika-tutorial/auspice/
——————————————————————————————————————————————————————————————————————————————
    The following datasets should be available in a moment:
       • http://127.0.0.1:4000/local/zika
——————————————————————————————————————————————————————————————————————————————
[...more output...]

Open the link shown in your browser.

Screenshot of Zika example dataset viewed in Nextstrain

Next steps