1. Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
- Author
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Emma B. Hodcroft, Misja Ilcisin, Elias Harkins, Richard A. Neher, Kairsten Fay, Trevor Bedford, Jover Lee, James Hadfield, John Huddleston, and Thomas R. Sibley
- Subjects
Phylogenetic tree ,Computer science ,610 Medicine & health ,Human pathogen ,Python (programming language) ,Bioinformatics ,Genome ,Article ,Variety (cybernetics) ,ComputingMethodologies_PATTERNRECOGNITION ,360 Social problems & social services ,Custom software ,Perl ,computer ,computer.programming_language - Abstract
Summary and statement of need 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.
- Published
- 2021
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