Nextstrain

Nextstrain

File:Nextstrain-logo-with-text-2023.svg

The Nextstrain logo

Nextstrain is an open-source project that provides a continually updated view of publicly available data on pathogen evolution. It is designed to help epidemiologists, researchers, and public health officials track the spread of infectious diseases by visualizing the genetic changes in pathogens over time.

Overview

Nextstrain integrates data from genomic sequencing with epidemiological information to create phylogenetic trees that illustrate the evolutionary relationships between different strains of a pathogen. This allows for real-time tracking of how diseases spread and evolve, which is crucial for understanding outbreaks and informing public health responses.

Features

Nextstrain offers several key features:

• Real-time tracking: By continuously updating with new genomic data, Nextstrain provides a dynamic view of pathogen evolution.
• Interactive visualizations: Users can explore phylogenetic trees and geographic maps to see how strains are related and where they have spread.
• Open-source platform: The project is open-source, allowing researchers to contribute data and improvements to the platform.

Applications

Nextstrain has been used to track a variety of pathogens, including:

• Influenza
• Ebola virus
• Zika virus
• SARS-CoV-2 (the virus responsible for COVID-19)

These applications have provided valuable insights into the transmission dynamics and mutation patterns of these viruses.

Technology

Nextstrain uses a combination of bioinformatics tools and cloud computing to process and visualize large datasets. The platform relies on augur for phylogenetic analysis and auspice for interactive visualization.

Community and Collaboration

Nextstrain is supported by a global community of researchers and public health officials. The project encourages collaboration and data sharing to improve the understanding of infectious disease dynamics.

Related pages

• Phylogenetics
• Epidemiology
• Genomic sequencing
• Public health