.. image:: https://github.com/houndry/barbet/blob/main/docs/images/barbet-banner.jpg?raw=true
.. start-badges
|pypi badge| |testing badge| |coverage badge| |docs badge| |black badge| |torchapp badge|
.. |pypi badge| image:: https://img.shields.io/pypi/v/barbet?color=blue
:alt: PyPI - Version
:target: https://pypi.org/project/barbet/
.. |testing badge| image:: https://github.com/houndry/barbet/actions/workflows/testing.yml/badge.svg
:target: https://github.com/houndry/barbet/actions
.. |docs badge| image:: https://github.com/houndry/barbet/actions/workflows/docs.yml/badge.svg
:target: https://houndry.github.io/barbet
.. |black badge| image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
.. |coverage badge| image:: https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/rbturnbull/09aad5114164b54daabe1f5efd02a009/raw/coverage-badge.json
:target: https://houndry.github.io/barbet/coverage/
.. |torchapp badge| image:: https://img.shields.io/badge/torch-app-B1230A.svg
:target: https://rbturnbull.github.io/torchapp/
.. end-badges
.. start-quickstart
Installation
==================================
Install using pip:
.. code-block:: bash
pip install git+https://github.com/houndry/barbet.git
Usage
==================================
See the options for making inferences with the command:
.. code-block:: bash
barbet --help
Run
==================================
.. code-block:: bash
barbet --input GCA_000006945.2.fna --output-dir outputs
Or using the large model:
.. code-block:: bash
barbet --input GCA_000006945.2.fna --output-dir outputs-large --large
Training
==================================
You can train the model on releases from GTDB or your own custom dataset.
See the instructions in the documentation for `preprocessing <https://houndry.github.io/barbet/preprocessing.html>`_ and `training <https://houndry.github.io/barbet/training.html>`_.
.. end-quickstart
Credits
==================================
.. start-credits
`Robert Turnbull <https://robturnbull.com>`_, Mar Quiroga, Gabriele Marini, Torsten Seemann, Wytamma Wirth
For more information contact: <wytamma.wirth@unimelb.edu.au>
Created using torchapp (https://github.com/rbturnbull/torchapp).
.. end-credits
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