.. PuMA documentation master file, created by
   sphinx-quickstart on Mon Jan 20 16:27:43 2020.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

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**Welcome to PuMA's documentation!**
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PuMA's code can be found `here. <https://github.com/KVD-lab/puma>`_ PuMA is also available through `iMicrobe. <https://www.imicrobe.us>`_

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About PuMA
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PuMA is a pipeline written in Python3 for papillomavirus genome annotation. 

The pipeline was created by utilizing several Python3 and command line packages including `Biopython <https://biopython.org>`_, `BLAST <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs>`_, `MEME, FIMO <https://meme-suite.org/>`_, and `MUSCLE <https://www.drive5.com/muscle>`_ as well as user defined functions. For more information on how PuMA works, refer to 'How PuMA Works'.

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Contents:
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.. toctree::
   :maxdepth: 7

   dependencies
   local_usage
   docker_usage
   iMicrobe_usage
   formatting
   output
   how_it_works
   license

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Support
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For questions, contact Dr. Koenraad Van Doorslaer via vandoorslaer AT arizona DOT edu or visit the KVD Lab `website <http://vandoorslaer.info>`_.