Nextstrain：实时追踪病原体进化。
Nextstrain: real-time tracking of pathogen evolution.
机构信息
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
出版信息
Bioinformatics. 2018 Dec 1;34(23):4121-4123. 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 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.
摘要
了解病原体的传播和演变对于有效的公共卫生措施和监测至关重要。Nextstrain 由病毒基因组数据库、系统发育分析的生物信息学管道以及交互式可视化平台组成。这些共同提供了对一系列具有高度公共卫生重要性的病毒病原体的进化和传播的实时视图。可视化将序列数据与地理信息、血清学或宿主物种等其他数据类型集成在一起。Nextstrain 将我们目前的理解编译到一个单一的可访问位置，向卫生专业人员、流行病学家、病毒学家和公众开放。
可用性和实施
所有代码（主要是 JavaScript 和 Python）均可从 github.com/nextstrain 免费获得，Web 应用程序可在 nextstrain.org 上使用。
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