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
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.
We recommend you configure either the docker or conda runtime for the workshop:
nextstrain setup conda
nextstrain setup docker
Check that everthing 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.
Overview and Basics
- Basics of phylogenetic analysis
- Exploring interactive phylogenies with Auspice
- The nextstrain toolchain
- Analysis with augur and Snakemake -- Virus tutorial
Next steps
- Analysis with augur and Snakemake -- SARS-CoV_2 Challenge
- Important steps in setting up your own analysis
Additional steps and details
- Options for time tree inference
- Specify color maps and geographic information
- Advanced snakemake (wildcards, functions, default rules)
- Parsing metadata from fasta files
- Community pages on nextstrain
Important links
- nextstrain.org
- nextstrain documentation
- Example repository with zika sequences
- Time-scaled phylogenies with TreeTime
- getting miniconda
- snakemake tutorial