overview.Rmd

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title: "Overview - Nemabiome.ca"
output: html_document
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<h1>Overview</h1>

<p>The information and protocols on this website are arranged under four broad sections which are accessible by clicking on the links on the top menu bar or on the titles of the boxes below. We aim to update this site as the development of the approach progresses and the number of applications increase. The aim is to enable any laboratory with basic parasitology and molecular biology capacity to undertake the approach.</p>

<div class="row">
	<div class="col-sm-3">
		<div class="panel panel-primary">
		  <div class="panel-heading">
		    <a class="panel-title" href="parasite.html">
    			<span class="ion ion-bug"></span>
		    	Parasite Prep
		    </a>
		  </div>
		  <div class="panel-body">
		  	<ul class="list-unstyled">
		  		<li><h6 class="text-left">Culture parasite material</h6></li>
		  		<li><h6 class="text-left">Prepare DNA lysates</h6></li>
		  	</ul>
		  </div>
		</div>
	</div>
	<div class="col-sm-3">
		<div class="panel panel-primary">
		  <div class="panel-heading">
		    <a class="panel-title" href="sequencing.html">
    			<span class="ion ion-erlenmeyer-flask"></span>
		    	Sequencing
		    </a>
		  </div>
		  <div class="panel-body">
		  	<ul class="list-unstyled">
		  		<li><h6 class="text-left">Amplify ITS-2 region and add adaptors</h6></li>
		  		<li><h6 class="text-left">Add Illumina barcodes</h6></li>
		  		<li><h6 class="text-left">Make normalized library and quantify</h6></li>
		  		<li><h6 class="text-left">Prepare and denature library</h6></li>
		  		<li><h6 class="text-left">Load library onto MiSeq instrument</h6></li>
		  	</ul>
		  </div>
		</div>
	</div>
	<div class="col-sm-3">
		<div class="panel panel-primary">
		  <div class="panel-heading">
		    <a class="panel-title" href="analysis.html">
		    	<span class="ion ion-monitor"></span>
		    	Analysis
		    </a>
		  </div>
		  <div class="panel-body">
		  	<ul class="list-unstyled">
			  	<li><h6 class="text-left">Download software and analysis files</h6></li>
			  	<li><h6 class="text-left">Download sequence data from Basespace</h6></li>
			  	<li><h6 class="text-left">Create sample list</li>
			  	<li><h6 class="text-left">Run analysis</li>
			  </ul>
		  </div>
		</div>
	</div>
	<div class="col-sm-3">
		<div class="panel panel-primary">
		  <div class="panel-heading">
		    <a class="panel-title" href="interpretation.html">
    			<span class="ion ion-stats-bars"></span>
		    	Interpretation 
		    </a>
		  </div>
		  <div class="panel-body">
		  	<ul class="list-unstyled">
			  	<li><h6 class="text-left">Visualize raw read count data in spreadsheet</h6></li>
			  	<li><h6 class="text-left">Quality control of raw read count data</h6></li>
			  	<li><h6 class="text-left">Correction for PCR bias</h6></li>
			  	<li><h6 class="text-left">Calculate the percentagage of each species</h6></li>
			  	<li><h6 class="text-left">Graphical visualization of species proportion data</h6></li>
		  	</ul>
		  </div>
		</div>
	</div>
</div>

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