EMUMADZ
=======

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Enhanced MUtation MApping and Detection in Zebrafish
----------------------------------------------------
.. whole_genome_sequencing documentation master file, created by
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   Copyright © 2025 <a href="https://orcid.org/0000-0002-9207-0385">Tyrone Chen <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-6435-7100">Richard Lupat <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0009-0005-5595-3882">Michelle Meier <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-6528-891X">Maia Zethoven <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-6130-250X">Gregory Baillie <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0000-0000-0000">Scott Paterson <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0009-0001-5651-1331">Oguzhan Baltaci <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0003-3147-8042">Cas Simons <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-1150-3549">Jason Li <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0003-4189-9422">Andrew Cox <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-8283-9760">Kelly Smith <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-0651-7065">Benjamin Hogan <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>

Code in this repository is provided under a `MIT license`_. This documentation is provided under a `CC-BY-4.0 license`_.

.. _MIT license: https://opensource.org/licenses/MIT

.. _CC-BY-4.0 license: https://creativecommons.org/licenses/by/4.0/

`Visit our lab website here.`_ Contact Benjamin Hogan at `ben.hogan@petermac.org`_.

.. _Visit our lab website here.: https://biomedicalsciences.unimelb.edu.au/sbs-research-groups/anatomy-and-physiology-research/stem-cell-and-developmental-biology/hogan-laboratory-vascular-developmental-genetics-and-cell-biology

.. _ben.hogan@petermac.org: mailto:ben.hogan@petermac.org

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    We thank <a href="https://orcid.org/0000-0002-9207-0385">Tyrone Chen <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-6435-7100">Richard Lupat <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0009-0005-5595-3882">Michelle Meier <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-6528-891X">Maia Zethoven <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0000-0000-0000">Song Li <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, <a href="https://orcid.org/0000-0002-3089-0871">Niko Thio <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a>, and <a href="https://orcid.org/0000-0002-1150-3549">Jason Li <img alt="ORCID logo" src="https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png" width="16" height="16" /></a> from the Bioinformatics Core (RRID: `SCR_025901`) at the Peter MacCallum Cancer Centre for their helpful comments and contributions to the pipeline.

Contains the documentation for our custom zebrafish whole genome sequencing pipeline.

.. toctree::
   :maxdepth: 3
   :caption: Contents:

   intro
   install
   case_study_1
   case_study_2
   case_study_3
   api

Appendix
========

.. toctree::
   :maxdepth: 1
   :caption: Appendix:
   
   appendix_internal_ref_only

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`