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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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<link rel="canonical" href="https://galaxyproject.eu/index-nanopore.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><br />
<img src="/assets/media/nanogalaxy_logo.png" height="100px" alt="NanoGalaxy logo" /></p>
<p>Welcome to <strong>NanoGalaxy</strong> – a webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies.</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>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>
<style type="text/css">
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<div align="center">
<table class="tg" width="50%">
<tr>
<th class="tg-0lax">
<div align="center">
<b>Polishing, QC and preprocessing</b><br />
<br />
<a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop" target="_top" title="Porechop">Porechop</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong" target="_top" title="Filtlong">Filtlong</a>, <a href="https://nanopore.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://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist" target="_top" title="Poretools">Poretools</a>,
<a href="https://nanopore.usegalaxy.eu/root?tool_id=https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/" target="_top" title="Medaka">Medaka</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/" target="_top" title="MultiQC">MultiQC</a>
</div>
</th>
<th class="tg-0lax" rowspan="4" align="center">
<img src="/assets/media/nanogalaxy_toolkit.png" height="400px" alt="NanoGalaxy toolkit" />
</th>
</tr>
<tr>
<td class="tg-0lax">
<div align="center"><b>Genome assembly</b><br />
<br />
<a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2" target="_top" title="Minimap2">Minimap2</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/miniasm" target="_top" title="Miniasm">Miniasm</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon" target="_top" title="Racon">Racon</a>
<br />
<a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon" target="_top" title="Racon">Racon</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye" target="_top" title="Flye">Flye</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler" target="_top" title="Unicycler">Unicycler</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/" target="_top" title="Wtdbg2">Wtdbg2</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu" target="_top" title="Canu">Canu</a>
</div>
</td>
</tr>
<tr>
<td class="tg-0lax">
<div align="center"><b>Visualisation</b><br />
<br />
<a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot" target="_top" title="Nanoplot">Nanoplot</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image" target="_top" title="Bandage">Bandage</a>
</div>
</td>
</tr>
<tr>
<td class="tg-0lax">
<div align="center"><b>Taxonomy and metagenomics</b><br />
<br />
<a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow" target="_top" title="PlasFlow">PlasFlow</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search" target="_top" title="Staramr">Staramr</a>, <a href="https://nanopore.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2" target="_top" title="Kraken2">Kraken2</a>
</div>
</td>
</tr>
</table>
</div>
<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>. These materials hosted on the GTN GitHub repository are available online at <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 available for all users.
The workflows can be extended using similar and alternative combinations using the Galaxy workflow editor.</p>
<p>The workflows are available in the <a href="https://nanopore.usegalaxy.eu/workflows/list_published" target="_top">Shared Workflows View</a> and are labeled with “<strong><em>ONT</em></strong>”.</p>
<table class="table-striped ont-workflow-table">
<tbody>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td><a href="https://nanopore.usegalaxy.eu/u/milad/w/nanopolish-variants-tutorial" target="_top"><img src="/assets/media/nanogalaxy-nanopolish.png" alt="Nanopolish workflow" /></a></td>
<td><a href="https://nanopore.usegalaxy.eu/u/milad/w/ont-assembly-flye-ahrens" target="_blank"><img src="/assets/media/nanogalaxy-ahrens.png" alt="Ahrens et. al workflow" /></a></td>
<td><a href="https://usegalaxy.eu/u/milad/w/workflow-wick-etal-ont" target="_blank"><img src="/assets/media/nanogalaxy-wick.png" alt="Wick et. al workflow " /></a></td>
<td><a href="https://nanopore.usegalaxy.eu/u/milad/w/metagenomics-krakan2" target="_top"><img src="/assets/media/nanogalaxy-kraken.png" alt="Metagenomics workflow" /></a></td>
</tr>
<tr>
<td>Basic workflows inspired by the Nanopolish tutorials</td>
<td>Genome assembly: Flye-based WF for highly repetitive genomes [Schmid et al. NAR 2018]</td>
<td>Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [Wick et al. Microbial genomics 2017]</td>
<td>Metagenomics: taxa classification</td>
</tr>
<tr>
<td><a href="https://usegalaxy.eu/u/milad/h/nanopolish-tutorial"><img src="https://img.shields.io/static/v1?label=history&message=view&color=blue" alt="Galaxy history" /></a> <a href="https://nanopore.usegalaxy.eu/u/milad/w/nanopolish-variants-tutorial"><img src="https://img.shields.io/static/v1?label=workflow&message=run&color=blue" alt="Galaxy workflow" /></a></td>
<td><a href="https://usegalaxy.eu/u/milad/h/ahrens-nanopore-gmmap"><img src="https://img.shields.io/static/v1?label=history&message=view&color=blue" alt="Galaxy history" /></a> <a href="https://nanopore.usegalaxy.eu/u/milad/w/ont-assembly-flye-ahrens"><img src="https://img.shields.io/static/v1?label=workflow&message=run&color=blue" alt="Galaxy workflow" /></a></td>
<td><a href="https://usegalaxy.eu/u/milad/h/wick-etal-nanopore"><img src="https://img.shields.io/static/v1?label=history&message=view&color=blue" alt="Galaxy history" /></a> <a href="https://usegalaxy.eu/u/milad/h/wick-etal-nanopore"><img src="https://img.shields.io/static/v1?label=workflow&message=run&color=blue" alt="Galaxy workflow" /></a></td>
<td><a href="https://usegalaxy.eu/u/milad/h/nanoporebeerdecodechimaytriple"><img src="https://img.shields.io/static/v1?label=history&message=view&color=blue" alt="Galaxy history" /></a> <a href="https://nanopore.usegalaxy.eu/u/milad/w/metagenomics-krakan2"><img src="https://img.shields.io/static/v1?label=workflow&message=run&color=blue" alt="Galaxy workflow" /></a></td>
</tr>
</tbody>
</table>
<hr />
<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
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</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>
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