Nextstrain real-time pathogen analysis: source code snapshot
Year: 2026
Type: software
Abstract: Source-code snapshot accompanying the manuscript "Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens" (Bioinformatics). It contains the source (without git history) of the Nextstrain core software packages (Augur, Auspice, Nextclade, the Nextstrain CLI, nextstrain.org, auspice.us) and the 22 per-pathogen real-time analysis workflow repositories described in the paper). The exact commit archived for each repository is listed in MANIFEST.tsv. The live, canonical, continuously updated source is at https://github.com/nextstrain. Each repository retains its own upstream open-source license (see LICENSE within each directory).
Authors: Andrews, Kimberly R., Chang, Jennifer, Roemer, Cornelius, Hadfield, James, Lin, Victor, Brito, Anderson F., Daodu, Richard Olumide, Joia, Isabel A., Kistler, Kathryn, Li, Allison, Moncla, Louise H., Paredes, Miguel I., Kühnert, Denise, Torres, Laura Marcela, Voitl, Laura, Aksamentov, Ivan, Hodcroft, Emma B., Huddleston, John, McCrone, John T., Anderson, John S. J., Sibley, Thomas R., Lee, Jover, Neher, Richard A., Bedford, Trevor
Institutions: Fred Hutch Cancer Center, SIB Swiss Institute of Bioinformatics, University of Basel, Howard Hughes Medical Institute, Instituto Todos pela Saúde, Robert Koch Institute, Freie Universität Berlin, University of Washington, University of Pennsylvania, Swiss Tropical and Public Health Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7212171320