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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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<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><br /></p>
<p>Welcome to the <strong>Erasmus MC</strong> Galaxy webserver.</p>
<ol id="markdown-toc">
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#tools" id="markdown-toc-tools">Tools</a></li>
<li><a href="#tutorials" id="markdown-toc-tutorials">Tutorials</a></li>
<li><a href="#workflows" id="markdown-toc-workflows">Workflows</a></li>
</ol>
<h1 id="get-started">Get started</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take <a href="https://nanopore.usegalaxy.eu/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<p>Check also the standard but customizable <a href="#workflows">workflows</a> available there.</p>
<h1 id="tools">Tools</h1>
<p><img src="/assets/media/nanogalaxy_toolkit.png" height="400px" alt="NanoGalaxy toolkit" /></p>
<p>A collection of best practice and popular tools are integrated (and are expanding) in this custom Galaxy instance. The ONT-oriented and -specific subset includes:</p>
<ul>
<li><strong>Polishing, QC and preprocessing</strong>
<ul>
<li><a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop" target="_top" title="Porechop">Porechop</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong" target="_top" title="Filtlong">Filtlong</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants" target="_top" title="Nanopolish">Nanopolish</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist" target="_top" title="Poretools">Poretools</a></li>
</ul>
</li>
<li><strong>Genome assembly</strong>
<ul>
<li><a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2" target="_top" title="Minimap2">Minimap2</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/miniasm" target="_top" title="Miniasm">Miniasm</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon" target="_top" title="Racon">Racon</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon" target="_top" title="Racon">Racon</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye" target="_top" title="Flye">Flye</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler" target="_top" title="Unicycler">Unicycler</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/" target="_top" title="Wtdbg2">Wtdbg2</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu" target="_top" title="Canu">Canu</a></li>
</ul>
</li>
<li><strong>Mapping</strong>
<ul>
<li><a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2" target="_top" title="Minimap2">Minimap2</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align" target="_top" title="GraphMap">GraphMap</a></li>
</ul>
</li>
<li><strong>Visualisation</strong>
<ul>
<li><a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot" target="_top" title="Nanoplot">Nanoplot</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image" target="_top" title="Bandage">Bandage</a></li>
</ul>
</li>
<li><strong>Taxonomy and metagenomics</strong>
<ul>
<li><a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow" target="_top" title="PlasFlow">PlasFlow</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search" target="_top" title="Staramr">Staramr</a>, <a href="https://erasmusmc.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2" target="_top" title="Kraken2">Kraken2</a></li>
</ul>
</li>
</ul>
<h1 id="tutorials">Tutorials</h1>
<p>We are passionate about training. So we are working in close collaboration with the <a href="https://galaxyproject.org/teach/gtn/" target="_blank">Galaxy Training Network (GTN)</a> to develop training materials of data analyses based on Galaxy <a class="citation" href="#batut2017community">(Batut <i>et al.</i>, 2017)</a>. The NanoGalaxy training materials are under development and will be soon hosted on the GTN GitHub repository <a href="https://training.galaxyproject.org" target="_blank">https://training.galaxyproject.org</a>.</p>
<h1 id="workflows">Workflows</h1>
<p>To orchestrate tools and help users with their analyses, some best practice workflows are prepared and become available. The workflows can be extended using similar and alternative combinations using the workflow editor.</p>
<p>The workflows are available in the <a href="https://nanopore.usegalaxy.eu/workflows/list_published" target="_top">Shared Workflows</a>, with the label “<strong><em>ONT</em></strong>”.</p>
<p>Some validated workflows:</p>
<ul>
<li>Basic workflows inspired by the Nanopolish tutorials
<br /> <a href="https://nanopore.usegalaxy.eu/u/milad/w/nanopolish-variants-tutorial" target="_top">workflow</a>
<img src="/assets/media/nanogalaxy-nanopolish.png" width="400px" alt="NanoGalaxy Nanopolish" /></li>
<li>Genome assembly:
<ul>
<li>
<p>Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]
Shared history: https://nanopore.usegalaxy.eu/u/milad/h/ahrens-nanopore-graphmap-minimap
<br /> <a href="https://nanopore.usegalaxy.eu/u/milad/w/ont-assembly-flye-ahrens" target="_blank">workflow</a>
<img src="/assets/media/nanogalaxy-ahrens.png" width="400px" alt="NanoGalaxy wf2" /></p>
</li>
<li>
<p>Unicycler-based WF for Klebsiella pneumoniae (Illumina and ONT) [Wick et al. Microbial genomics 2017]
Shared history: https://nanopore.usegalaxy.eu/u/milad/h/wick-etal</p>
</li>
</ul>
</li>
<li>Metagenomics: taxa classification
<br /> <a href="https://nanopore.usegalaxy.eu/u/milad/w/metagenomics-krakan2" target="_top">workflow</a>
<img src="/assets/media/nanogalaxy-kraken.png" width="400px" alt="NanoGalaxy wf2" /></li>
</ul>
<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>
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<tr>
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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.
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cookie to identify your data. This cookie is not used for any other purposes
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If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
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<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>
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