These features are deprecated, which means they are no longer maintained and will go away in a future major version of Augur. They are currently still available for backwards compatibility, but should not be used in new code.

augur parse preference of name over strain as the sequence ID field

Deprecated in February 2024. Planned to be reordered June 2024 or after.

Currently, augur parse checks for a ‘name’ field and then a ‘strain’ field to use as a sequence ID. This order will be changed in favor of searching for a ‘strain’ and then a ‘name’ field to be more consistent with the rest of Augur.

Users who have both ‘name’ and ‘strain’ fields in their data, and want to favor using the ‘name’ field should add the following augur parse parameter --output-id-field 'name'.


Deprecated in December 2023. Planned for removal March 2024 or after.

This is part of a larger effort to formalize Augur’s Python API.

We recognize the existing usage of this function, so it has been moved to

augur export v1

Deprecated in version 22.2.0 (July 2023). Planned for removal January 2024 or after.

augur export v2 was introduced in Augur version 6.0.0. Migrate by following the official guide.

augur ancestral --output

Deprecated in version 5.2.0 (December 2019). Removed in version 7.0.0 (April 2020).

--output was replaced by --output-node-data to accommodate the addition of --output-sequences.