===================================================================================
BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit
===================================================================================

**BEDOPS** is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

You can read more about **BEDOPS** and how it can be useful for your research in the :ref:`Overview <overview>` documentation, as well as in the `original manuscript <http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract>`_.

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========
Citation
========

If you use **BEDOPS** in your research, please cite the following manuscript:

   Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. **BEDOPS: high-performance genomic feature operations**. *Bioinformatics* (2012) 28 (14): 1919-1920. `doi: 10.1093/bioinformatics/bts277 <http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract>`_

========
Contents
========

.. toctree::
   :numbered:

   content/overview
   content/installation
   content/revision-history
   content/usage-examples
   content/performance
   content/reference
   content/summary
   content/release

.. |header| raw:: html

   <h1>BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit</h1>

.. |about_html| raw:: html

   <br><strong>BEDOPS</strong> is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

   <p>You can read more about <strong>BEDOPS</strong> and how it can be useful for your research in the <a href="content/overview.html">Overview</a> documentation, as well as in the <a href="http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract">original manuscript</a>.</p><br>

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   <br><img src="_static/quick_start.png" style="height:150px;">

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         <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
            <li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/bedops_linux_x86_64-v2.4.36.tar.bz2">x86-64 (64-bit)</a> binaries</li>
            <li><a href="content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
         </ul>
      </div>
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         <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
            <li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/BEDOPS.2.4.36.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
            <li><a href="content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
         </ul>
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            <li><a href="https://github.com/bedops/bedops/archive/v2.4.36.tar.gz">Source code</a> (tar.gz)</li>
            <li><a href="https://github.com/bedops/bedops/archive/v2.4.36.zip">Source code</a> (zip)</li>
            <li><a href="content/installation.html#installation-via-source-code">Compilation instructions</a></li>
         </ul>
      </div>
   </div>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/bedops_linux_x86_64-v2.4.36.tar.bz2">x86-64 (64-bit)</a> binaries</li>
   <li><a href="content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/BEDOPS.2.4.36.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
   <li><a href="content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="https://github.com/bedops/bedops/archive/v2.4.36.tar.gz">Source code</a> (tar.gz)</li>
   <li><a href="https://github.com/bedops/bedops/archive/v2.4.36.zip">Source code</a> (zip)</li>
   <li><a href="content/installation.html#installation-via-source-code">Compilation instructions</a></li>
   </ul>

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   <img src="_static/reference_v2.png" style="height:36px; margin:0; width:auto !important;">
   <div class="index_cols">
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         <img src="_static/set_operations_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
         <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:2px; padding-right:0px; padding-left:20px;">
            <li><a href="content/reference/set-operations/bedops.html"><tt>bedops</tt></a> - apply set operations on any number of BED inputs</li>
            <li><a href="content/reference/set-operations/bedextract.html"><tt>bedextract</tt></a> - efficiently extract BED features</li>
            <li><a href="content/reference/set-operations/closest-features.html"><tt>closest-features</tt></a> - matches nearest features between BED files</li>
        </ul>
      </div>
      <div class="col_element">
         <img src="_static/statistics_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
         <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:2px; padding-right:0px; padding-left:20px;">
            <li><a href="content/reference/statistics/bedmap.html"><tt>bedmap</tt></a> - map overlapping BED elements onto target regions and optionally compute any number of common statistical operations</li>
         </ul>
      </div>
      <div class="col_element">
         <img src="_static/file_management_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
         <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:2px; padding-right:0px; padding-left:20px;">
            <li><a href="content/reference/file-management/sorting/sort-bed.html"><tt>sort-bed</tt></a> - apply lexicographical sort to BED data</li>
            <li><a href="content/reference/file-management/compression/starch.html"><tt>starch</tt></a> and <a href="content/reference/file-management/compression/unstarch.html"><tt>unstarch</tt></a> - compress and extract BED data</li>
            <li><a href="content/reference/file-management/compression/starchcat.html"><tt>starchcat</tt></a> - merge compressed archives</li>
            <li><a href="content/reference/file-management/compression/starchstrip.html"><tt>starchstrip</tt></a> - filter archive by chromosomes</li>
            <li><a href="content/reference/file-management/conversion.html">Conversion tools</a> - convert common genomic formats to BED</li>
         </ul>
      </div>
   </div>
   <div class="index_cols">
      <div class="col_element">
         <img src="_static/performance_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
         <ul style="list-style-type:square; font-size:smaller; margin:0; margin-right:2px; padding-right:0px; padding-left:20px;">
            <li>Parallel <a href="content/reference/file-management/conversion/parallel_bam2bed.html"><tt>bam2bed</tt></a> and <a href="content/reference/file-management/conversion/parallel_bam2starch.html"><tt>bam2starch</tt></a> - parallelized conversion and compression of BAM data</li>
            <li><a href="content/performance.html#set-operations-with-bedops">Set operations with <tt>bedops</tt></li>
            <li><a href="content/performance.html#compression-characteristics-of-starch">Compression characteristics of <tt>starch</tt></li>
            <li><a href="content/performance.html#independent-testing">Independent testing</a></li>
         </ul>
      </div>
      <div class="col_element">
          <img src="_static/toc_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
          <ul style="list-style-type:square; font-size:smaller; margin:0; margin-right:2px; padding-right:0px; padding-left:20px;">
             <li><a href="content/summary.html">Table summary</a> of <strong>BEDOPS</strong> toolkit</li>
             <li><a href="content/reference/file-management/compression/starch-specification.html">Starch v2.2</a> format specification</li>
             <li><a href="content/reference/set-operations/nested-elements.html">About nested elements</a>
             <li><a href="content/revision-history.html">Revision history</a></li>
             <li><a href="content/release.html">Github release instructions</a></li>
             <li><a href="https://github.com/bedops/bedops">Github repository</a></li>
          </ul>
      </div>
      <div class="col_element">
          <img src="_static/support_v2.png" style="height:130px; margin:0; width:auto !important; margin-bottom:12px;">
          <ul style="list-style-type:square; font-size:smaller; margin:0; margin-right:2px; padding-right:0px; padding-left:20px;">
             <li><a href="content/installation.html">How to install <strong>BEDOPS</strong></a></li>
             <li><a href="content/usage-examples.html">Usage examples</a> of <strong>BEDOPS</strong> tools in action</li>
             <li><a href="http://bedops.uwencode.org/forum/"><strong>BEDOPS</strong> user forum</a></li>
             <li><a href="http://groups.google.com/group/bedops-discuss"><strong>BEDOPS</strong> discusssion mailing list</a></li>
          </ul>
      </div>
   </div>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="content/reference/set-operations/bedops.html"><tt>bedops</tt></a> - apply set operations on any number of BED inputs</li>
   <li><a href="content/reference/set-operations/bedextract.html"><tt>bedextract</tt></a> - efficiently extract BED features</li>
   <li><a href="content/reference/set-operations/closest-features.html"><tt>closest-features</tt></a> - matches nearest<br/>features between BED files</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="content/reference/statistics/bedmap.html"><tt>bedmap</tt></a> - map overlapping BED elements onto target regions and optionally compute any number of common statistical operations</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="content/reference/file-management/sorting/sort-bed.html"><tt>sort-bed</tt></a> - apply lexicographical sort to BED data</li>
   <li><a href="content/reference/file-management/compression/starch.html"><tt>starch</tt></a> and <a href="content/reference/file-management/compression/unstarch.html"><tt>unstarch</tt></a> - compress and extract BED data</li>
   <li><a href="content/reference/file-management/compression/starchcat.html"><tt>starchcat</tt></a> - merge compressed archives</li>
   <li><a href="content/reference/file-management/compression/starchstrip.html"><tt>starchstrip</tt></a> - filter archives by chromosome names</li>
   <li><a href="content/reference/file-management/conversion.html">Conversion tools</a> - convert common genomic formats to BED</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li>Parallel <a href="content/reference/file-management/conversion/parallel_bam2bed.html"><tt>bam2bed</tt></a> and <a href="content/reference/file-management/conversion/parallel_bam2starch.html"><tt>bam2starch</tt></a> - parallelized conversion and compression of BAM data</li>
   <li><a href="content/performance.html#set-operations-with-bedops">Set operations with <tt>bedops</tt></li>
   <li><a href="content/performance.html#compression-characteristics-of-starch">Compression characteristics of <tt>starch</tt></li>
   <li><a href="content/performance.html#independent-testing">Independent testing</a></li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="content/installation.html">How to install <strong>BEDOPS</strong></a></li>
   <li><a href="content/usage-examples.html">Usage examples</a> of <strong>BEDOPS</strong> tools in action</li>
   <li><a href="http://bedops.uwencode.org/forum/"><strong>BEDOPS</strong> user forum</li>
   <li><a href="http://groups.google.com/group/bedops-discuss"><strong>BEDOPS</strong> discusssion mailing list</li>
   </ul>

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   <ul style="list-style-type:square; font-size:smaller; margin:10px; padding:0;">
   <li><a href="content/summary.html">Table summary</a> of <strong>BEDOPS</strong> toolkit</li>
   <li><a href="content/reference/file-management/compression/starch-specification.html">Starch v2.2</a> format specification</li>
   <li><a href="content/reference/set-operations/nested-elements.html">About nested elements</a>
   <li><a href="content/revision-history.html">Revision history</a></li>
   <li><a href="content/release.html">Github release instructions</a></li>
   <li><a href="https://github.com/bedops/bedops">Github repository</a></li>
   </ul>
