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Nextstrain: real-time tracking of pathogen evolution

Nextstrain: real-time tracking of pathogen evolution SummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

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Publisher
Oxford University Press
Copyright
© The Author(s) 2018. Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/bty407
Publisher site
See Article on Publisher Site

Abstract

SummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

Journal

BioinformaticsOxford University Press

Published: Dec 1, 2018

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