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Nextstrain: real-time tracking of pathogen evolution

By James Hadfield, Colin Megill, Sidney M. Bell, John Huddleston, Barney I Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher

Posted 22 Nov 2017
bioRxiv DOI: 10.1101/224048 (published DOI: 10.1093/bioinformatics/bty407)

Summary: Understanding 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 visualisation 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, publicly available for use by health professionals, epidemiologists, virologists and the public alike. Availability and implementation: All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

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