Huddleston John, Hadfield James, Sibley Thomas R, Lee Jover, Fay Kairsten, Ilcisin Misja, Harkins Elias, Bedford Trevor, Neher Richard A, Hodcroft Emma B
Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
J Open Source Softw. 2021;6(57). doi: 10.21105/joss.02906. Epub 2021 Jan 7.
The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.
对人类病原体的分析需要多种生物信息学工具。这些工具包括标准的基因组和系统发育软件，以及为处理病毒和细菌相对数量众多且较短的基因组而开发的定制软件。研究人员越来越依赖这些工具的输出结果来推断人类疾病的传播动态，并向公共卫生官员提出可行的建议（布莱克等人，2020年；加迪等人，2015年）。为了能够对病原体进化进行实时分析，生物信息学工具必须随着样本数量的增加而迅速扩展，并且要有足够的灵活性以适应各种问题和生物体。为满足这些需求，我们开发了Augur，这是一个用于人类病原体系统发育分析的生物信息学工具包。
