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. 2018 Dec 1;34(23):4121-4123.
doi: 10.1093/bioinformatics/bty407.

Nextstrain: real-time tracking of pathogen evolution

James Hadfield  1 , Colin Megill  1 , Sidney M Bell  1   2 , John Huddleston  1   2 , Barney Potter  1 , Charlton Callender  1 , Pavel Sagulenko  3 , Trevor Bedford  1 , Richard A Neher  3   4   5
Affiliations

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al. Bioinformatics. .

Abstract

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 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 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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Figures

Fig. 1.
Fig. 1.
Genomic epidemiology of Zika virus as of Oct 2017 (live display at nextstrain.org/zika). The main interface consists of three linked panels—a phylogenetic tree, geographic transmissions and the genetic diversity across the genome
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