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<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8'>
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<meta name="description" content="mmgenome : Tools for extracting individual genomes from metagneomes">
<link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
<title>mmgenome</title>
</head>
<body>
<!-- HEADER -->
<div id="header_wrap" class="outer">
<header class="inner">
<a id="forkme_banner" href="/~https://github.com/MadsAlbertsen/mmgenome">View on GitHub</a>
<h1 id="project_title">mmgenome</h1>
<h2 id="project_tagline">Tools for extracting individual genomes from metagneomes</h2>
<section id="downloads">
<a class="zip_download_link" href="/~https://github.com/MadsAlbertsen/mmgenome/zipball/master">Download this project as a .zip file</a>
<a class="tar_download_link" href="/~https://github.com/MadsAlbertsen/mmgenome/tarball/master">Download this project as a tar.gz file</a>
</section>
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<section id="main_content" class="inner">
<h3>
<a name="what-is-mmgenome" class="anchor" href="#what-is-mmgenome"><span class="octicon octicon-link"></span></a>What is mmgenome?</h3>
<p>The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the <a href="http://madsalbertsen.github.io/multi-metagenome/">multi-metagenome</a> concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format. </p>
<p>The mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as "yet another binning method", but rather a package to integrate different binning strategies. </p>
<p>The package is currently in beta stage and we'll be updating the documentation here shortly. All functions in the mmgenome R package has associated documentation, check it out in R by e.g. <code>?mmplot</code>.</p>
<h3>
<a name="how-does-it-work" class="anchor" href="#how-does-it-work"><span class="octicon octicon-link"></span></a>How does it work?</h3>
<p>Check out our examples of <a href="http://madsalbertsen.github.io/mmgenome/Load_data.html">loading data</a> and <a href="http://madsalbertsen.github.io/mmgenome/Genome_extraction.html">extracting genomes</a> in the mmgenome R package. The associated Rmarkdown files can be found in the folder mmgenome/workflows.</p>
<h3>
<a name="getting-started" class="anchor" href="#getting-started"><span class="octicon octicon-link"></span></a>Getting started</h3>
<p>Install the latest version of <a href="http://www.r-project.org/">R (>3.1)</a>, <a href="http://www.r-project.org/">Rtools</a> and <a href="http://www.rstudio.com/">RStudio</a>. Then go ahead and install the mmgenome R package directly from github using the devtools package.</p>
<pre><code>install.packages("devtools")
devtools::install_github("MadsAlbertsen/mmgenome/mmgenome")
</code></pre>
<p>You might need to install <code>Biostrings</code> through <code>bioconductor</code> depending on your version of R. However, it's quite easily done.</p>
<pre><code>source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
</code></pre>
<p>To generate your own data simply clone repository and setup the shell script mmgenome/workflows/data.generation.2.1.0.sh.</p>
<pre><code>git clone /~https://github.com/MadsAlbertsen/mmgenome.git
</code></pre>
</section>
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<p class="copyright">mmgenome maintained by <a href="/~https://github.com/MadsAlbertsen">MadsAlbertsen</a></p>
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