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ORFanage: By-reference ORF annotation
=================================
    
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**ORFanage** is an ultra-efficient pseudo-alignment algorithm for annotating ORFs by maximizing similarity to reference proteins.

-------------------

**Example**

.. figure:: content/images/template.png

	For each overlap **ORFanage** extends coordinates towards the 3’ and 5’ ends based on suitable parameters. 

.. code-block:: console
	
	$ orfanage --reference genome.fasta --output output.gtf \
		--query query.gtf reference.gtf

**ORFanage** allows users to rapidly search and find ORFs on query transcripts.
Users may apply the method to their experimental datasets to:

- Search for likely coding transcripts
- Discover novel protein variants
- Identify and quantify AS events involved in any observed changes to the protein sequnces
- Much more

The method can also be applied to correct available protein annotations at loci with additional reference data.

The User Guide
--------------

.. toctree::
   :maxdepth: 2

   user/install
   user/orfanage
   user/orfcompare
   user/file_formats
   user/examples
   user/contact