Welcome to Maize_paper's documentation!
=======================================


About this scripts
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This directory contains most of script used in 'A new fungal threat to maize: host-range expansion of Pyricularia oryzae from a common weed'. For assembly, masking of repeated elements and annotation, a new, more user-friendly  pipeline has been developed.


.. toctree::
   :caption: Assembly Script
   :name: Assembly_Script
   :maxdepth: 2

   Assembly.rst

.. toctree::
   :caption: Secretome Selection
   :name: Secretome_Selection
   :maxdepth: 2

   Secretome.rst

.. toctree::
   :caption: Annotation pipeline
   :name: Annotation_pipeline
   :maxdepth: 2

   Annotation.rst

.. toctree::
   :caption: Pangenome analysis
   :name: Pangenome_analysis
   :maxdepth: 2

   Pangenome.rst

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`