Analysis Modules
================

The following sections describe each analysis available in Ensembl Anno.

Repeat annotation
-----------------

.. toctree::
   :maxdepth: 1

   red
   dust
   trf
   repeatmasker

Simple feature annotation
-------------------------

.. toctree::
   :maxdepth: 1

   cpg
   eponine

Small ncRNA annotation
----------------------

.. toctree::
   :maxdepth: 1

   cmsearch
   trnascan

Transcriptomic annotation
-------------------------

.. toctree::
   :maxdepth: 1

   star
   stringtie
   scallop
   minimap

Protein annotation
------------------

.. toctree::
   :maxdepth: 1

   genblast
   miniprot