##################
Related software
##################

Bedtools has been used as an engine behind other genomics software and has been 
integrated into widely used tools such as Galaxy and IGV.  Below is a likely
incomplete list.  If you know of others, please let us know, or better yet,
edit the document on GitHub and send us a pull request.  You can do this by
clicking on the "Edit and improve this document" link in the lower lefthand
corner.


-------------------
IGV
-------------------
Bedtools is now integrated into the IGV genome viewer as of IGV version 2.2.  We
are actively working withe IGV development team to improve and expand this 
integration.  See 
`here <http://www.broadinstitute.org/igv/IGV2.2.x>`_
and 
`here <https://www.broadinstitute.org/software/igv/bedtools>`_ for details.

    .. image:: images/bedtoolsMenu.png

-------------------
Galaxy
-------------------

`Galaxy <https://main.g2.bx.psu.edu/>`_ has its own tools for working with
genomic intervals under the "Operate on Genomic Intervals" section.  A subset
of complementary Bedtools utilities have also been made available on Galaxy in
an effort to provide functionality that isn't available with the native Galaxy 
tools.

    .. image:: images/galaxy-bedtools.png


-------------------
Pybedtools
-------------------

`Pybedtools <http://pypi.python.org/pypi/pybedtools>`_ is a really fantastic 
Python library that wraps (and extends upon) the bedtools utilities and exposes 
them for easy use and new tool development using Python.  Pybedtools is actively 
maintained by Ryan Dale.


-------------------
MISO
-------------------

`MISO <http://genes.mit.edu/burgelab/miso/>`_ is "a probabilistic framework 
that quantitates the expression level of alternatively spliced genes from 
RNA-Seq data, and identifies differentially regulated isoforms or exons across 
samples." A subset of the functionality in MISO depends upon ``bedtools``. MISO
is developed by Yarden Katz.


-------------------
RetroSeq
-------------------

`RetroSeq <http://bioinformatics.oxfordjournals.org/content/early/2012/12/10/bioinformatics.bts697.abstract>`_
is "a tool for discovery and genotyping of transposable element variants (TEVs) 
(also known as mobile element insertions) from next-gen sequencing reads aligned 
to a reference genome in BAM format". RetroSeq is developed by Thomas Keane. 
Source code can be obtained on `GitHub <https://github.com/tk2/RetroSeq>`_.

-------------------------
Intersphinx documentation
-------------------------
BEDTools documentation pages are available via Intersphinx (http://sphinx-doc.org/ext/intersphinx.html).
To enable this, add the following to conf.py in a Sphinx proejct:

    intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}
    
BEDtools documentation links can then be generated with e.g.:

    :ref:`BEDTools:map <bedtools:map>`
    
