This workshop provides on overview on 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
Overview
- Basics of phylogenetic analysis
- Exploring interactive phylogenies with Auspice
- The nextstrain toolchain
- Analysis with augur and Snakemake -- Virus tutorial
- Analysis with augur and Snakemake -- Bacteria Tutorial
- Important steps in setting up your own analysis
Important links
- nextstrain.org
- nextstrain documentation
- Example repository with zika sequences
- Time-scaled phylogenies with TreeTime
- getting miniconda
- snakemake tutorial