Parts of a whole¶
Augur is a series of composable, modular bioinformatics tools. We use these to create recipes for different pathogens and different analyses, which can be reproduced given the same input data and replicated when new data is available.
Auspice is a web-based visualization program, to present and interact with phylogenomic and phylogeographic data. Auspice is what you see when, for example, you visit nextstrain.org/mumps/na.
Augur produces dataset files which are visualized by Auspice. These files are often referred to as “JSONs” colloquially because they use a generic data format called JSON.
Builds are recipes of code and data that produce result datasets for visualization and analysis. Builds run dozens of commands and often use Snakemake to manage the pipeline workflow, but any workflow system can be used, such as Nextflow or WDL. As an example, our core builds are organized as Git repositories hosted on GitHub which contain a Snakemake workflow using Augur, configuration, and data.
nextstrain.org is a web application to host and present the core pathogen builds maintained by the Nextstrain team, as well as builds published to Nextstrain Groups and community pages which are maintained and shared by many other people. The website incorporates a customized version of Auspice for displaying each dataset.
You can run Augur and Auspice on your own computer and use them independently or together with your own builds, our core builds, or others’ group or community builds. You can even install Auspice on your own web server if you don’t want to host your builds via nextstrain.org.
The Nextstrain CLI (a program called
together all of the above to provide a consistent way to run pathogen builds,
access Nextstrain tools like Augur and Auspice across computing environments
such as Docker, Conda, and AWS Batch, and publish datasets to nextstrain.org.
Nextclade is a web application and two command-line
nextalign) for performing viral genome
alignment, mutation calling, clade assignment, quality checks, and phylogenetic
placement. Nextclade can be used indepedently of other Nextstrain tools as
well as integrated into builds.