Bonsai
======

Bonsai is a web app for visualising the output from the bacterial analysis pipeline `jasen <https://github.com/genomic-medicine-sweden/JASEN>`_ as well as performing cluster analysis, annotation, and more. Bonsai is a multi-user application for collaborating on analysing outbreaks and antibiotic resistance of human pathogenic bacteria.

.. note::

   Bonsai is under active development and in alpha stage. Expect limited documentation, breaking changes, and bugs until the official 1.0 release.

Check out the :doc:`installation` section for installation instructions.

.. toctree::
   :maxdepth: 2

   /installation
   /container_configuration
   /administration
   /deployment
   /lims_export
   /faq

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Developer guide

   /dev/index
   /dev/login_systems
   /dev/minhash
   /dev/allele_clustering

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Reference

   /changelog