.. RBGE's core pipelines documentation master file, created by
   sphinx-quickstart on Thu Aug  5 15:03:09 2021.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

RBGE's bioinformatics and data management 
=============================================

Here you will find information about genomic data management and tutorials of the most common bioinformatics pipelines used at the Royal Botanic Garden Edinburgh, RBGE.


.. toctree::
   :maxdepth: 1
   :caption: Wet Laboratory:

   wet_labbook_template

.. toctree::
   :maxdepth: 1
   :caption: Data management:

   setup
   wheretostore
   wheretorun
   installsoftware

.. toctree::
   :maxdepth: 1
   :caption: Quality of the raw reads:

   rawreads
   fastqc
   trimmomatic
   cutadapt
   
.. toctree::
   :maxdepth: 1
   :caption: Target Capture:

   mapping
   aligning
   phylogeny

.. toctree::
   :maxdepth: 1
   :caption: Contact:
   
   contact

.. toctree::
   :maxdepth: 1
   :caption: Transcriptomics:


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

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