A command-line application used for phylogenetic analysis. Documentation
A web application used for phylogenetic visualization and analysis. Documentation
also pathogen workflow, pathogen analysis, Nextstrain workflow
A reproducible process comprised of one or more builds producing datasets, which can be visualized by Auspice. Implementation varies per workflow, but generally they are run by workflow managers such as Snakemake.
Our core workflows can be divided into two types:
Single-build workflow (e.g. Zika workflow): one build producing one dataset.
Multi-build workflow (e.g. SARS-CoV-2 workflow): multiple builds producing multiple datasets.
The individual builds in a multi-build workflow are also “workflows” in the definition of workflow managers like Snakemake.
- core workflow
A workflow maintained by the Nextstrain team.
- workflow repository
also pathogen workflow repository
A version-controlled folder containing all files necessary to run a workflow.
also Nextstrain build
(noun) A sequence of commands, parameters and input files which work together to reproducibly execute bioinformatic analyses and generate a dataset for visualization with Auspice.
- build (verb)
A general term for running a workflow (e.g.
- build step
A modular instruction of a build which can be run standalone (e.g.
augur filter), often with clear input and output files.
also Auspice JSONs
A collection of JSONs produced by a build. It is also the shared file prefix of the JSONs. For example
flu/seasonal/h3n2/ha/2yidentifies a dataset which corresponds to the files :
Some workflows produce a single, synonymous dataset, like Zika. Others, like seasonal flu, produce many datasets.
A method of data-driven storytelling with interactive views of datasets displayed alongside multiple pages (or slides) of text and images. Saved as a Markdown file with extended syntax to support additional displays.
Viewable on nextstrain.org or with Auspice via the nextstrain view or auspice view commands.
See also Communicating Results Using Narratives and Writing a narrative.
.jsonfiles produced by Augur and visualized by Auspice. These files make up a dataset. See data formats.
- Nextstrain CLI
The Nextstrain command-line interface (Nextstrain CLI) provides a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across runtimes such as Docker, Conda, and AWS Batch.
also Nextstrain runtime
When installing and using the Nextstrain CLI, there are different configuration options, or runtimes, depending on the operating system.
Ambient runtime (formerly “native”)
AWS Batch runtime (only for