Module 3.4 – Walking through Nextstrain trees

Overview: This module demonstrates how to navigate through Nextstrain phylogenetic trees using various functionalities such as filtering, zooming, coloring and labeling to further analyze SARS-CoV-2 genomic epidemiological data. Nextstrain provides a list of SARS-CoV-2 resourcesexternal icon and publicly available analyses to help explore their tool.

Posted: 03/12/21

Presenter: Krisandra Allen, MPH, MB(ASCP)^CM (view bio)
Molecular Epidemiologist
Washington State Department of Health

Download Presentation Slides pdf icon[PDF – 18 slides]

Further Reading:

1. Nextstrain SARS-CoV-2 resources.external icon
   Nextstrain, updated 2021.

Additional Resources:

1. Auspice: An open-source interactive tool for visualising phylogenomic data.external icon
   Nextstrain, updated 2020.
2. SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES).external icon
   Updated 2021.

Hands-on Example:

1. Phylogenetic tree.external icon
2. Metadata table. Module 3.4 Demo Meta Data [CSV, 1KB]external icon
   Note: Please first convert ToolkitModule_3.4-demoData.csv into a tsv file, according to the instructions here.external icon