Glossary

Augur

A command-line application used for phylogenetic analysis. Documentation

Auspice

A web application used for phylogenetic visualization and analysis. Documentation

workflow

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:

  1. Single-build workflow (e.g. Zika workflow): one build producing one dataset.

  2. Multi-build workflow (e.g. SARS-CoV-2 workflow): multiple builds producing multiple datasets.

Note

The individual builds in a multi-build workflow are also β€œworkflows” 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.

build

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. nextstrain build).

build step

A modular instruction of a build which can be run standalone (e.g. augur filter), often with clear input and output files.

dataset

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/2y identifies a dataset which corresponds to the files :

  • flu_seasonal_h3n2_ha_2y_meta.json

  • flu_seasonal_h3n2_ha_2y_tree.json

  • flu_seasonal_h3n2_ha_2y_tip-frequencies.json

Some workflows produce a single, synonymous dataset, like Zika. Others, like seasonal flu, produce many datasets.

narrative

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.

JSONs

Special .json files 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, Native, and AWS Batch.

Documentation

runtime

also Nextstrain runtime

When installing and using the Nextstrain CLI, there are different configuration options, or runtimes, depending on the operating system.

  1. Docker runtime

  2. Native runtime

  3. AWS Batch runtime (only for nextstrain build)