Description
===========

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    <iframe width="640" height="360" src="https://www.youtube.com/embed/8p753IcdImI" frameborder="0" allowfullscreen></iframe>

`ASCIIGenome` is a command-line genome browser running from terminal window and solely based on
ASCII characters. Since `ASCIIGenome` does not require a graphical interface it is particularly
useful for  quickly visualizing genomic data on remote servers. The idea is to make `ASCIIGenome`
the Vim  of genome viewers.

The closest program to `ASCIIGenome` is probably `samtools tview <http://samtools.sourceforge.net/tview.shtml>`_ but 
`ASCIIGenome` offers much more flexibility, similar to popular GUI viewers like the `IGV browser <https://www.broadinstitute.org/igv/>`_.

Some key features:

* Command line input and interaction, no graphical interface, minimal installation.
* Can load multiple files in various :ref:`formats <Supported_input_and_output>`.
* Can access remote files via URL or ftp address.
* Easy navigation and searching of features and sequence motifs and filtering options.
* Support for BS-Seq alignment.

Getting help
------------

Feel free to send any comment, bug, or issues to one or more of the following:

* Open an issue on `GitHub <https://github.com/dariober/ASCIIGenome/issues>`_ 
* Post a question on `Biostars.org <https://www.biostars.org/>`_ or `bioinformatics.stackexchange.com <https://bioinformatics.stackexchange.com/>`_ (recommended: send a notification email to :code:`dario<dot>beraldi<at>gmail<dot>com` so I read the question).
* Send email to :code:`dario<dot>beraldi<at>gmail<dot>.com`

.. image:: screenshots/composite.png

How to cite
-----------

If you happen to find `ASCIIGenome` useful and you would like to acknowledge it, please quote the
GitHub repository (https://github.com/dariober/ASCIIGenome/). 

An article describing `ASCIIGenome` has been published in `Bioinformatics <https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx007/2949507/ASCIIGenome-A-command-line-genome-browser-for?redirectedFrom=fulltext>`_ .

Credits
-------

* Bam processing is mostly done with the `samtools/htsjdk <https://github.com/samtools/htsjdk>`_ library.
* Bigwig and tdf are processed with classes from `IGV <https://github.com/igvteam/igv>`_ source code.
* Block compression and indexing done using `jvarkit <https://github.com/lindenb/jvarkit>`_.
* Brew installation thanks to `dalloliogm <https://github.com/dalloliogm>`_.

.. image:: screenshots/ex3.png