Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
Creators
- 1. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- 2. Biozentrum, University of Basel, Basel, Switzerland
- 3. Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
Description
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.
Files
Files
(11.2 MB)
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