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index-covid19.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://galaxyproject.eu/index-covid19.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
<script src="/assets/js/jquery-3.2.1.slim.min.js" integrity="sha256-k2WSCIexGzOj3Euiig+TlR8gA0EmPjuc79OEeY5L45g=" crossorigin="anonymous"></script>
<script src="/assets/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<h1 id="welcome-to-covid19usegalaxyeu">Welcome to covid19.usegalaxy.eu</h1>
<p>This subdomain of covid19.usegalaxy.eu is devoted to research on coronavirus disease 2019 (COVID-19), which has recently been declared a pandemic by the World Health Organization.</p>
<p>This subdomain servers as a companion to our study describing the analysis of early COVID-19 data, the goal of which is to underscore the importance of access to raw data and demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid reproducible research during global crises.</p>
<p>This subdomain contains the exact versions of all software used.</p>
<p>Our analysis was divided into six parts listed below. Each part has a dedicated page that provides links to input datasets, intermediate and final results, workflows, and Galaxy histories that list all details for each analysis. These workflows can be re-run on this subdomain.</p>
<ol>
<li><a href="1-PreProcessing">Pre-processing of raw read data</a></li>
<li><a href="2-Assembly">Assembly of SARS-CoV-2 genome</a></li>
<li><a href="3-MRCA">Estimation of timing for most recent common ancestor (MRCA)</a></li>
<li><a href="4-Variation">Analysis of variation within individual isolates</a></li>
<li><a href="5-S-analysis">Analysis of Spike protein substitutions</a></li>
<li><a href="6-RecombinationSelection">Analysis of recombination and selection</a></li>
</ol>
<p>In addition we will be looking at newly released data here → <a href="updates">Updates: Analysis of additional data</a></p>
<h2>Our Data Policy</h2>
<table class="table table-striped">
<thead>
<tr>
<th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th>
</tr>
</thead>
<tbody>
<tr>
<td>User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
</td>
<td>Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
</td>
<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
</td>
<td>The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td>
</tr>
</tbody>
</table>
<!-- <h4>Registered Users</h4>
User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
<h4>Unregistered Users</h4>
Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
<h4>FTP Data</h4>
Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
-->
<div>
<iframe style="border: 0px" width="100%" height="150px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=1" ></iframe>
</div>
<div>
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</div>
<div class="row">
<section class="section-content">
<div class="col-md-12">
</div>
</section>
</div>
</div>
</div>
</div>
</div>
<footer class="navbar-default">
<div class="container">
<div class="row">
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<p>UseGalaxy.eu is maintained largely by the <a href="/freiburg/">Freiburg Galaxy Team</a> but also collectively by groups and individuals from across Europe. All of the member sites in this repository contribute to the European Galaxy Project.
For <strong>acknowledgement</strong>, please refer to the <a href="/about">About</a> section.
All content on this site is available under <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0-1.0</a> unless otherwise specified.</p>
</div>
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<ul class="contact-info">
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu/website/tree/master/index-covid19.md">Edit this page on GitHub</a></li>
<li><i class="fa fa-envelope"></i><a href="mailto:[email protected]">[email protected]</a></li>
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu">usegalaxy-eu</a></li>
<li><img class="fa-mastodon" src="/assets/media/mastodon.svg" style="width:18px;height:18px;padding-right:4px;filter:grayscale(100%);-webkit-filter:grayscale(100%);"/><a href="https://bawü.social/@galaxyfreiburg">galaxyfreiburg</a></li>
<li><i class="fa fa-rss"></i>Subscribe <a href="/feed.xml">via RSS (UseGalaxy.eu Feed)</a></li>
</ul>
</div>
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</div>
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</body>
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