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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
<!-- Compiled and minified CSS -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/1.0.0/css/materialize.min.css">
<title>Bacterial Genomics Project</title>
<link rel="icon" type="image/svg" href="/docs/images/dna-icon.svg">
<style>
body {
background-color: white;
color: black;
}
a, a:visited {
color: black;
}
nav, nav .nav-wrapper {
background-color: #24B064; /* Darker shade for nav bar */
}
.nav-wrapper a.brand-logo, .nav-wrapper ul li a {
color: white; /* Ensuring nav text is white */
}
</style>
</head>
<body>
<nav class="green">
<div class="nav-wrapper container">
<a href="#" class="brand-logo">Bacterial Genomics</a>
<ul class="right hide-on-med-and-down">
<li><a href="https://github.com/bacterial-genomics">Overview</a></li>
<li><a href="https://github.com/orgs/bacterial-genomics/repositories">Repositories</a></li>
<li><a href="#contact">Contact</a></li>
</ul>
</div>
</nav>
<main class="container">
<div class="grid">
<section>
<h1><b>Welcome to the Bacterial Genomics Page</b></h1>
<u><a href="https://github.com/bacterial-genomics">Bacterial Genomics Github Page</a></u>
<h3 id="repositories">Key Repositories</h3>
<p>Our GitHub repository hosts a wide range of resources, including assembly workflows, analysis tools, and various tools we use for our research. Here are some of our notable repositories:</p>
<ul>
<u><li><a href="https://github.com/bacterial-genomics/wf-paired-end-illumina-assembly">Assembly Workflow Repository</a></li></u>
<u><li><a href="https://github.com/bacterial-genomics/wf-assembly-snps">Assembly SNP Workflow Repository</a></li></u>
<u><li><a href="https://github.com/bacterial-genomics/leptospira_type_strains">Leptospira Type Strains Repository</a></li></u>
</ul>
<h3>Assembly Workflow</h3>
<p>This workflow assembles bacterial isolate genomes from paired-end Illumina FastQ files. Post-assembly contig correction is performed, and a variety of quality assessment processes are recorded throughout the workflow.</p>
<img src="docs/images/wf-paired-end-illumina-assembly_logo_light.png" width="900" height="50"><br>
<img src="docs/images/updated_wf_asm_image.png" width="1400" height="500"><br>
<u><a href="https://bacterial-genomics.github.io/wf-paired-end-illumina-assembly/">Assembly Workflow Documentation</a></u><br>
<u><a href="https://bacterial-genomics.github.io/wf-paired-end-illumina-assembly/docs/output.html">Assembly Workflow Output Documentation</a></u>
<h3>Assembly-based SNP Workflow</h3>
<p>General workflow for genome assembly-based SNP phylogeny with optional recombination masking.</p>
<img src="wf-assembly-snps/docs/images/wf-assembly-snps_logo_light.png" width="500" height="50"><br>
<img src="docs/images/wf-assembly-snps_workflow.png" width="700" height="500"><br>
<u><a href="https://github.com/bacterial-genomics/wf-assembly-snps/blob/main/README.md">Assembly SNP Workflow Documentation</a></u><br>
<u><a href="https://github.com/bacterial-genomics/wf-assembly-snps/blob/main/docs/output.md">Assembly SNP Workflow Output Documentation</a></u><br>
<h4 id="contact">Contact & Collaboration</h4>
<ul>
<li><u><a href="https://github.com/taylorpaisie/wf-paired-end-illumina-assembly/blob/main/.github/CONTRIBUTING.md">Contributing Guidelines</a></u></li>
<li><u><a href="https://github.com/bacterial-genomics/wf-paired-end-illumina-assembly/blob/dev/ADD_MODULE_GUIDE.md">How to Add a Module</a></u></li>
</ul>
<p>If you're interested in contributing to the project or have any inquiries, please reach out to us:</p>
</section>
</div>
</main>
<section aria-label="Subscribe example">
<div class="container">
<article>
<hgroup>
<h4>Stay Updated</h4>
<h4>Subscribe for updates</h4>
</hgroup>
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<form class="grid" action="subscribe.php" method="post">
<input type="text" id="firstname" name="firstname" placeholder="Your Name" aria-label="Your Name" required />
<input type="email" id="email" name="email" placeholder="Your Email" aria-label="Your Email" required />
<button type="submit">Subscribe</button>
</form>
</article>
</div>
</section>
<footer class="container">
<small>
<a href="https://github.com/bacterial-genomics">GitHub</a> • <a href="#">Privacy Policy</a>
</small>
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