Module 3.4 – Walking through Nextstrain trees

What to know

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.

thumbnail for module 3.4

Overview

Presenter: Krisandra Allen, MPH, MB(ASCP)CM | Molecular Epidemiologist Washington State Department of Health
Download Presentation Slides [PDF - 19 slides]

Nextstrain provides a list of SARS-CoV-2 resources and publicly available analyses to help explore their tool.

Further Reading

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

Additional Resources

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

Hands-on Example

  1. Phylogenetic tree.
  2. Metadata table. Module 3.4 Demo Meta Data [CSV, 1KB] Note: Please first convert ToolkitModule_3.4-demoData.csv into a tsv file, according to the instructions here.
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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)