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    <title>Ragout - enlarge your contigs!</title>
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          <h1>Ragout</h1>
          <h2>A tool for assisted assembly using multiple references</h2>
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        <p><center><img src="images/ragout.png"/></center></p>

          <p>Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
assisted assembly using multiple references. It takes a short read
assembly (a set of contigs), a set of related references
and a corresponding phylogenetic tree and then assembles the contigs into
scaffolds.</p>

<p>The benefits of assembly with multiple references become significant,
when those references have structural variations compared to the target
genome. Even if each reference is structurally divergent, it is possible
to assemble the target into the correct set of scaffolds. Enlarge your
contigs with Ragout!</p>

<p>The current version of Ragout was mostly tested on bacterial genomes,
however it also contains an experimental support of mamalian-scaled ones.</p>

<h2>
<a name="installation" class="anchor" href="#installation"><span class="octicon octicon-link"></span></a>Installation</h2>

<p>Latest version: 0.3 beta (Jun 22 2014)</p>

<p>Read detailed installation instructions <em><a href="install.html">here</a></em>.</p>

<h2>
<a name="manual" class="anchor" href="#manual"><span class="octicon octicon-link"></span></a>Manual</h2>

<p>Please read it <em><a href="usage.html">here</a></em>.</p>

<h2>
<a name="authors" class="anchor" href="#authors"><span class="octicon octicon-link"></span></a>Authors</h2>

<ul>
<li>Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of
Sciences)</li>
<li>Son Pham (University of California, San Diego)</li>
<li>Pavel Avdeyev (St. Petersburg University of the Russian Academy of
Sciences)</li>
<li>Dmitry Meleshko (St. Petersburg University of the Russian Academy of
Sciences)</li>
</ul><h2>
<a name="citation" class="anchor" href="#citation"><span class="octicon octicon-link"></span></a>Citation</h2>

<p>If you use Ragout for your research, please cite:</p>

<ul>
<li>Mikhail Kolmogorov, Brian Raney, Benedict Paten, and Son Pham. 
"Ragout: A reference-assisted assembly tool for bacterial genomes" 
(accepted to ISMB 2014)</li>
</ul><h2>
<a name="ismb-2014-supplementary" class="anchor" href="#ismb-2014-supplementary"><span class="octicon octicon-link"></span></a>ISMB 2014 supplementary</h2>

<p>Supplementary materials for ISMB submission could be found at:
<a href="https://drive.google.com/file/d/0B1pUguR1yn7TMjNpX09JdFphT3c/edit?usp=sharing">https://drive.google.com/file/d/0B1pUguR1yn7TMjNpX09JdFphT3c/edit?usp=sharing</a></p>

<h2>
<a name="contacts" class="anchor" href="#contacts"><span class="octicon octicon-link"></span></a>Contacts</h2>

<p>Please report any bugs directly to the issue tracker of this project.
Also, you can send your feedback at <a href="mailto:fenderglass@gmail.com">fenderglass@gmail.com</a></p>

<h2>
<a name="acknowledgements" class="anchor" href="#acknowledgements"><span class="octicon octicon-link"></span></a>Acknowledgements</h2>

<p>The work was partially supported by VP Foundation.</p>

<p>We would like to thank:</p>

<ul>
<li>Nikolay Vyahhi (testing and some useful suggestions)</li>
<li>Tamara Panesh (art)</li>
<li>Aleksey Gurevich (testing)</li>
</ul><h2>
<a name="license" class="anchor" href="#license"><span class="octicon octicon-link"></span></a>License</h2>

<p>Ragout itself is distributed under BSD license, but the package also contains
some third-party software. Most of this software is completely free to redistribute,
but some such as Sibelia or Newick parser are released under the GPL. We therefore release
Ragout distribution under the GPL and note that the licenses of the constituent
packages can be viewed in their subfolders. (see <em>LICENSE</em> file)</p>

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