Nextstrain: Difference between revisions

Latest revision as of 05:50, 16 February 2025

Nextstrain[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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-{{DISPLAYTITLE:Nextstrain}}
+== Nextstrain ==
-'''Nextstrain''' is an open-source project that provides a continually updated view of publicly available data on pathogen evolution. It is a powerful tool used by researchers, epidemiologists, and public health officials to track the spread and evolution of infectious diseases, such as [[SARS-CoV-2]], [[Influenza]], and [[Ebola virus]].
+[[File:Nextstrain-logo-with-text-2023.svg|thumb|right|The Nextstrain logo]]
-==Overview==
+'''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.
-Nextstrain integrates data from [[genomic sequencing]] with powerful visualization tools to provide insights into the dynamics of pathogen spread. The platform is designed to be accessible and informative, offering a real-time view of how pathogens are evolving and spreading across the globe.
-==History==
+== Overview ==
-Nextstrain was developed by a team led by [[Trevor Bedford]] and [[Richard Neher]]. The project began as a response to the need for real-time tracking of pathogen evolution during outbreaks. It gained significant attention during the [[2014 West Africa Ebola outbreak]] and has since been applied to numerous other pathogens.
-==Features==
+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.
-===Real-time Tracking===
+== Features ==
-Nextstrain provides real-time tracking of pathogen evolution by integrating genomic data from various sources. This allows for the visualization of how a pathogen is spreading geographically and temporally.
-===Phylogenetic Analysis===
+Nextstrain offers several key features:
-The platform uses [[phylogenetic trees]] to show the evolutionary relationships between different strains of a pathogen. This helps in understanding how different strains are related and how they have evolved over time.
-===Interactive Visualizations===
+* '''Real-time tracking''': By continuously updating with new genomic data, Nextstrain provides a dynamic view of pathogen evolution.
-Nextstrain offers interactive visualizations that allow users to explore data in detail. Users can zoom in on specific regions, view metadata associated with each strain, and observe changes in the pathogen's genetic makeup.
+* '''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.
-===Open Source and Community Driven===
+== Applications ==
-Nextstrain is open-source, meaning that its code is freely available for anyone to use, modify, and contribute to. The project encourages collaboration and contributions from the global scientific community.
-==Applications==
+Nextstrain has been used to track a variety of pathogens, including:
-Nextstrain has been used in various public health contexts, including:
-* Tracking the global spread of [[COVID-19]] and identifying new variants of concern.
+* [[Influenza]]
-* Monitoring seasonal influenza and aiding in vaccine strain selection.
+* [[Ebola virus]]
-* Understanding the dynamics of [[Zika virus]] outbreaks.
+* [[Zika virus]]
+* [[SARS-CoV-2]] (the virus responsible for [[COVID-19]])
-==Impact==
+These applications have provided valuable insights into the transmission dynamics and mutation patterns of these viruses.
-Nextstrain has had a significant impact on the field of [[epidemiology]] and public health. By providing a platform for real-time data sharing and analysis, it has improved the ability of researchers and public health officials to respond to outbreaks more effectively.
+== 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 ==
-==Also see==
-* [[Genomic epidemiology]]
 * [[Phylogenetics]]
-* [[Pathogen evolution]]
+* [[Epidemiology]]
-* [[Public health informatics]]
+* [[Genomic sequencing]]
+* [[Public health]]
-{{Infectious disease control}}
-{{Epidemiology}}
 [[Category:Bioinformatics]]
 [[Category:Public health]]
-[[Category:Open science]]
+[[Category:Open-source software]]
-{{No image}}