Deprecated

These features are deprecated, which means they are no longer maintained and will go away in a future major version of Augur.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 filter options --output and -o

Deprecated in version 29.1.0. Planned for removal October 2025 or after.

--output and -o are aliases to --output-sequences. They will be removed to avoid confusion with other output options.

xopen major version 1

Deprecated in version 25.1.0 (July 2024). Removed in version 27.0.0 (December 2024).

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

Deprecated in version 24.2.0 (February 2024). Reordered in version 26.0.0 (September 2024).

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'.

augur.utils.read_strains

Deprecated in version 24.0.0 (January 2024). Removed in version 29.0.0 (February 2025).

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.io.read_strains.

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.