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 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
- Analysis with augur and Snakemake -- SARS-CoV_2 solutions
- Analysis with augur and Snakemake -- Bacteria Tutorial
- 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