========================
FaST-reference
========================

This command should be run before processing a library, in order to build the appropriate reference.
FaST-reference requires the reference genome fasta file and a annotation file in gtf format.
For human and mouse, if the fasta and gtf files are not provided, FaST-reference will instead download 
these information from Gencode website, defaulting to the latest release. However, you can specify a
given release of the Gencode data.
Currently the only supported species are human and mouse, but support for custom genomes will be
added soon.



Usage
-------------------

Command syntax:

.. code-block:: bash

   $ FaST-reference -s <species>  [ -v gencode_version | -f genome.fa -g annotation.gtf ] 




===========   ===================
Option         Description
===========   ===================
**-s** 	      Mandatory. Currently either 'human' or 'mouse'.
**-v**        Optional, gencode annotation version (i.e. 'v46' for human version 46, 'vM25' for mouse version 25).
	      If omitted and no fasta or gtf are selected, the latest Gencode release for the selected species will be 
	      downloaded.
**-f**	      Optional. Path to a fasta file corresponding to the species of interest. FaST-reference does not expect
	      a compressed fasta file, in case you have a fa.gz (or otherwise compressed file) it is up to you 
	      extracting it before running FaST-reference. If omitted, Gencode data for the selected species 
	      will be downloaded.
**-g**        Optional, Path to gtf format file containing transcriptome annotation for the selected species. 
	      FaST-reference does not expect a compressed gtf file, in case you have a gtf.gz (or otherwise 
	      compressed file) it is up to you  extracting it before running FaST-reference. If omitted, the Gencode 
	      data for the selected species will be downloaded.
===========   ===================


	
Notes
-------------------
	
* If you do not have a local fasta and gtf file, internet connection will be required to download Gencode data.
* If specifying a local fasta and/or gtf file please make sure that they correspond to the same genome assembly.
* If specifying only a fasta (or gtf) file, please make sure that they match the same genome assembly of
  the Gencode gtf (or fasta) that FaST-reference will download (the latest available if -v is omitted).