GAMBIT Documentation
********************


GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for
rapid taxonomic identification of microbial pathogens. It uses an efficient genomic distance
metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI
`RefSeq`_) to identify genome assemblies from across the Bacterial kingdom in seconds.

- `Project Homepage <homepage_>`_
- `Publication in PLOS One <publication_>`_
- `Reproducible workflow to generate all analyses and figures in the paper <gambit_pub_>`_

If you have any questions or feedback about the project or its documentation please contact me at
jared@jaredlumpe.com, I would love to hear them.

.. _RefSeq: https://www.ncbi.nlm.nih.gov/refseq/
.. _homepage: https://github.com/jlumpe/gambit
.. _publication:  https://doi.org/10.1371/journal.pone.0277575
.. _gambit_pub: https://github.com/jlumpe/gambit-publication


Contents
========

.. toctree::
   :maxdepth: 1

   install
   tutorial
   cli
   databases
   api/api