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index-phage.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">
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<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<link rel="canonical" href="https://galaxyproject.eu/index-phage.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">
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</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><img src="/assets/media//phage_usegalaxy_banner_1.png" alt="phage galaxy banner" /></p>
<h1 id="welcome-to-the-phage-galaxy">Welcome to the Phage Galaxy!</h1>
<p><strong>Phage Galaxy</strong> is a web platform to analyze phage data. This includes tools useful for next-generation sequence assembly, annotation pipelines, comparative analyses, and genome visualization. Here you will find all the software produced by the <a href="https://cpt.tamu.edu">Center for Phage Technology at Texas A&M University</a>. To get started, visit our tutorials below.</p>
<p><strong>Phage Galaxy</strong> is still under development! Links to our annotation workflows will be made avalable once they are fully functional.</p>
<h1 id="resources">Resources</h1>
<h2 id="phage-annotation-pipeline">Phage Annotation Pipeline</h2>
<p>The latest robust structural and functional annotation workflows are available under Shared Data > Workflows. Our workflows are all labeled with the <strong>CPT</strong> tag for easy searching.</p>
<h2 id="apollo-annotator">Apollo annotator</h2>
<p>The Phage Galaxy is connected to Apollo via the Apollo Bridge tools, which allow Galaxy to read and write data in the Apollo instance that is also hosted by usegalaxy.eu. Apollo can be accessed from within Galaxy or directly via the link below. You must be logged in to usegalaxy.eu to use Apollo.</p>
<div align="center">
<a href="https://phage.usegalaxy.eu/apollo/" target="_blank">
<button type="button" class="btn btn-primary btn-lg">Phage Galaxy Apollo</button>
</a>
</div>
<h2 id="tutorials-list">Tutorials list</h2>
<p>Our training material in Galaxy Tranining Network format is tailored specifically to phage analysis, including identification of introns and lysis genes. Our training modules describe the use of Galaxy, Apollo, and our tools and workflows. We also have a user FAQ that answers questions about Galaxy and Apollo usage for phage annotation.</p>
<div align="center">
<a href="https://cpt.tamu.edu/training-material/" target="_blank">
<button type="button" class="btn btn-primary btn-lg">CPT Training Tutorials</button>
</a>
</div>
<h2 id="video-help">Video help</h2>
<p>We have also made a number of videos that describe some of our tools and workflows. These are available at our YouTube channel below.</p>
<div align="center">
<a href="https://www.youtube.com/channel/UCSg8OW817LvhnjU3grTgRNQ" target="_blank">
<button type="button" class="btn btn-primary btn-lg">CPT YouTube channel</button>
</a>
</div>
<h1 id="references">References</h1>
<p>If you are publishing using the CPT phage tools or annotation workflows, please cite the following publication:</p>
<blockquote>
<p>Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, Hu JC, Young R, Gill JJ. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLoS Comput Biol. 2020 v16(11):e1008214. doi: 10.1371/journal.pcbi.1008214. <a href="https://pubmed.ncbi.nlm.nih.gov/33137082/">PMID: 33137082</a>; <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660901/">PMCID: PMC7660901</a>.</p>
</blockquote>
<p>Individual tools may also have additional citations listed.</p>
<h1 id="contact">Contact</h1>
<p>This phage tools and workflows on Phage Galaxy are maintained by the <a href="https://cpt.tamu.edu">Center for Phage Technology</a>. For more information contact jason.gill@tamu.edu.</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>.
-->
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<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>
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