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<a href="http://github.com/jts/sga">Fork me on GitHub</a>
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<h1><a href="http://github.com/jts/sga">sga</a>
<span class="small">by <a href="http://github.com/jts">jts</a></span></h1>
<div class="description">
experimental de novo sequence assembler using string graphs
</div>
<p>
SGA is a de novo sequence assembler based on the assembly string graph [1]. It is implemented as a collection of algorithms
based on the FM-index/Burrows-Wheeler transform. This includes the efficient FM-index to string graph construction algorithm described in [2].
The package also contains programs to correct sequencing errors and remove duplicate reads without using a reference genome.
<h2>Dependencies</h2>
<ul>
<li>google-sparsehash (http://code.google.com/p/google-sparsehash/)</li>
<li> zlib (www.zlib.net)</li>
</ul>
<h2>License</h2>
<p>GPLv3</p>
<h2>References</h2>
<ol>
<li>E.W. Myers. The fragment assembly string graph. <em>Bioinformatics</em>. 21(suppl_2):ii79–85, 2005. <a href="http://www.ncbi.nlm.nih.gov/pubmed/16204131">[Pubmed]</a></li>
<li>J.T. Simpson, R. Durbin. Efficient construction of an assembly string graph using the FM-index. <em>Bioinformatics</em>, 26(12):i367-373, 2010. <a href="http://www.ncbi.nlm.nih.gov/pubmed/20529929">[Pubmed]</a></li>
</ol>
<h2>Authors</h2>
<p>Jared Simpson (js18[-at-]sanger.ac.uk)<br/></p>
<h2>Download</h2>
<p>
You can download this project in either
<a href="http://github.com/jts/sga/zipball/master">zip</a> or
<a href="http://github.com/jts/sga/tarball/master">tar</a> formats.
</p>
<p>You can also clone the project with <a href="http://git-scm.com">Git</a>
by running:
<pre>$ git clone git://github.com/jts/sga</pre>
</p>
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get the source code on GitHub : <a href="http://github.com/jts/sga">jts/sga</a>
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