Huddleston, John; Hadfield, James; Sibley, Thomas R; Lee, Jover; Fay, Kairsten; Ilcisin, Misja; Harkins, Elias; Bedford, Trevor; Neher, Richard A; Hodcroft, Emma B. (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), p. 2906. Open Journals 10.21105/joss.02906
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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.
Item Type: |
Journal Article (Original Article) |
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Division/Institute: |
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM) |
UniBE Contributor: |
Hodcroft, Emma Britt |
Subjects: |
600 Technology > 610 Medicine & health 300 Social sciences, sociology & anthropology > 360 Social problems & social services |
ISSN: |
2475-9066 |
Publisher: |
Open Journals |
Language: |
English |
Submitter: |
Andrea Flükiger-Flückiger |
Date Deposited: |
07 Jul 2021 23:14 |
Last Modified: |
21 Jun 2023 15:57 |
Publisher DOI: |
10.21105/joss.02906 |
PubMed ID: |
34189396 |
BORIS DOI: |
10.48350/157387 |
URI: |
https://boris.unibe.ch/id/eprint/157387 |
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