nextstrain view

Visualizes a completed pathogen builds or narratives in Auspice, the Nextstrain visualization app.

<path> may be a dataset (.json) file or narrative (.md) file to start Auspice and directly open the specified dataset or narrative in a browser. Adjacent datasets and/or narratives may also be viewable as an appropriate data directory for Auspice is automatically inferred from the file path.

<path> may also be a directory with one of the following layouts:

├── auspice/
│   └── *.json
└── narratives/
    └── *.md

├── auspice/
│   └── *.json
└── *.md

├── *.json
└── narratives/
    └── *.md

├── *.json
└── *.md

Dataset and narrative files will be served, respectively, from auspice and/or narratives subdirectories under the given <path> if the subdirectories exist. Otherwise, files will be served from the given directory <path> itself.

If your pathogen build directory follows our conventional layout by containing an auspice directory (and optionally a narratives directory), then you can give nextstrain view the same path as you do nextstrain build.

Note that by convention files named or will be ignored for the purposes of finding available narratives.

usage: nextstrain view [options] <path>
       nextstrain view --help

Positional Arguments


Path to a directory containing dataset JSON and/or narrative Markdown files for Auspice, or a directory containing an auspice/ and/or narratives/ directory, or a specific dataset JSON or narrative Markdown file.

Named Arguments

--help, -h

Show a brief help message of common options and exit


Open a web browser automatically

Default: False


Do not open a web browser automatically (the default)

Default: True


Allow other computers on the network to access the website (alias for –host=


Listen on the given hostname or IP address instead of the default “”

Default: “”


Listen on the given port instead of the default port 4000

Default: 4000

runtime selection options

Select the Nextstrain runtime to use, if the default is not suitable.


Run commands inside a container image using Docker. (default)


Run commands in the ambient environment, outside of any container image.


Run commands with access to a fully-managed Conda environment.


Run commands inside a container image using Singularity.

development options

These should generally be unnecessary unless you’re developing Nextstrain.


Container image name to use for the Nextstrain runtime (default: “nextstrain/base” for Docker and AWS Batch, docker://nextstrain/base for Singularity)

Default: “nextstrain/base”


Program to run inside the runtime

Default: “auspice”

development options for –docker


Replace the image’s copy of augur with a local copy


Replace the image’s copy of auspice with a local copy


Replace the image’s copy of fauna with a local copy


Replace the image’s copy of sacra with a local copy


Additional arguments to pass to docker run

Default: []