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index-assembly.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-assembly.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">
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<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">
<p><img src="/assets/media/logo_assembly.png" alt="Anna's hummingbird photo courtesy of [VJAnderson](https://commons.wikimedia.org/wiki/File:Anna%27s_Hummingbird,_Washington_State_03.jpg)" class="sc-intro-left" /></p>
<h1 class="no_toc" id="welcome-to-galaxy-for-genome-assembly">Welcome to Galaxy for Genome Assembly</h1>
<p>The <strong>Genome Assembly Workbench</strong> is a comprehensive set of analysis tools and consolidated workflows to assist in Genome Assembly.
The workbench is based on the <a href="https://galaxyproject.org" target="_blank">Galaxy framework</a>,
which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.</p>
<h2 id="vertebrate-genomes-project">Vertebrate Genomes Project</h2>
<p>The workbench is optimized to include all data, tools, and workflows associated with the <strong><a href="https://vertebrategenomesproject.org/">Vertebrate Genomes Project (VGP)</a></strong>. All raw data published by the VGP is available from the remote data repository <strong>Genome Ark</strong> in the data uploader. The VGP assembly workflows are available from the <strong>Workflows</strong> tab within <strong>Shared Data</strong>. As new assemblies are generated, they will appear in <strong>Histories</strong> in the <strong>Shared Data</strong> tab. Currently, we have assembled <strong><b>23</b></strong> genomes.</p>
<h2 id="human-pangenome-reference-project">Human Pangenome Reference Project</h2>
<p>The workbench has partnered with the <strong><a href="https://humanpangenome.org/">Human Pangenome Reference Consortium (HPRC)</a></strong> to provide the latest genome assembly resources for the generation of high-quality diploid reference genomes. High-quality human datasets are available through the consortium, including multiple datatypes for the <a href="https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0">HG002</a> benchmark and dozens of individuals from the <a href="https://github.com/human-pangenomics/HPP_Year1_Assemblies">1000 Genomes Project</a>. All data can directly be imported in Galaxy as input to the workflows.</p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#vertebrate-genomes-project" id="markdown-toc-vertebrate-genomes-project">Vertebrate Genomes Project</a></li>
<li><a href="#human-pangenome-reference-project" id="markdown-toc-human-pangenome-reference-project">Human Pangenome Reference Project</a></li>
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#vgp-assembly-training" id="markdown-toc-vgp-assembly-training">VGP assembly training</a> <ol>
<li><a href="#additional-training-material" id="markdown-toc-additional-training-material">Additional training material</a></li>
</ol>
</li>
<li><a href="#partners" id="markdown-toc-partners">Partners</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
<a href="https://assembly.usegalaxy.eu/tours/core.galaxy_ui" target="_blank"><strong>guided tour</strong></a> through Galaxy’s user interface.</p>
<h1 id="vgp-assembly-training">VGP assembly training</h1>
<p>As a result of a collaboration with the VGP team, the Galaxy Training Network has made available two trainings which goal is to describe the VGP pipeline through two complementary approaches: a step-by-step version, and a workflow-focused short version. In the extended version, each of the steps required to run the VGP pipeline is descussed in detail, with particular attention to the algorithms and parameters. On the other hand, the short version provides a quick walkthrough on how the workflows can be used to rapidly assemble a genome using the VGP pipeline with the Galaxy Workflow System.</p>
<div align="center">
<a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" target="_blank"><button type="button" class="btn btn-primary btn-lg">VGP Step-by-Step Training</button></a>
<a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_workflow_training/tutorial.html" target="_blank"><button type="button" class="btn btn-primary btn-lg">VGP Workflow-Focused Training</button></a>
<a href="https://assembly.usegalaxy.eu/u/gallardoalba/h/vgp-example-history"><button type="button" class="btn btn-primary btn-lg">Open example history</button></a>
</div>
<p><br /></p>
<h2 id="additional-training-material">Additional training material</h2>
<p>All relevant materials for <a href="https://training.galaxyproject.org/training-material/search?query=assembly">assembly-related data analysis</a> can also be found within the GTN.</p>
<table class="table table-striped">
<thead>
<tr>
<th>Lesson</th>
<th>Slides</th>
<th>Hands-on</th>
<th>Input dataset</th>
<th>Workflows</th>
<th>Galaxy History</th>
</tr>
</thead>
<tbody>
<tr>
<td>Welcome and introduction to Galaxy</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://training.galaxyproject.org/training-material/videos/watch.html?v=introduction/tutorials/galaxy-intro-short/slides" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>An Introduction to Genome Assembly</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>A deeper look into Genome Assembly algorithms</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/algorithms-introduction/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Quality Control</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://youtu.be/BWonTPS4zB8" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://youtu.be/QJRlX2hWDKM" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.61771" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://assembly.usegalaxy.eu/u/gallardoalba/h/quality-control" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Mapping</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/slides.html" target="_blank"><i class="fa fa-slideshare" aria-hidden="true"></i></a> / <a href="https://youtu.be/7FhHb8EV3EU" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a> / <a href="https://youtu.be/1wm-62E2NkY" target="_blank"><i class="fa fa-video-camera" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1324070" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://assembly.usegalaxy.eu/u/gallardoalba/h/mapping" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>K-mer coverage</td>
<td> </td>
<td> </td>
<td> </td>
<td><a href="https://assembly.usegalaxy.eu/u/delphine-l/w/kcov" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://assembly.usegalaxy.eu/u/delphine-l/h/kcov-1" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Salsa Scaffolding</td>
<td> </td>
<td> </td>
<td> </td>
<td><a href="https://assembly.usegalaxy.eu/u/delphine-l/w/salsa-scaffolding" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://assembly.usegalaxy.eu/u/delphine-l/h/salsa-scaffolding" target="_blank"><i class="fa fa-list-ul" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Chloroplast genome assembly</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>De Bruijn Graph Assembly</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Genome Assembly of MRSA using Illumina MiSeq Data</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Genome Assembly of MRSA using Oxford Nanopore MinION Data</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Making sense of a newly assembled genome</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Unicycler Assembly</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>SARS-CoV-2 assembly with removing human reads</td>
<td><a href="https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p><br /></p>
<p>If you want to know more about the GTN or how to become part of the Galaxy community, check the videos below!</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/lDqWxzWNk1k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="">
</iframe>
<iframe width="560" height="315" src="https://www.youtube.com/embed/-1MPdxmRs8U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
<p><br /></p>
<h1 id="partners">Partners</h1>
<p>This service is a joint project between different groups from the <a href="https://vertebrategenomesproject.org" target="_blank">Vertebrate Genomes Project (VGP)</a>, the <a href="https://vertebrategenomesproject.org/erga" target="_blank">European Reference Genome Atlas project</a>, the <a href="https://humanpangenome.org/">Human Pangenome Reference Consortium (HPRC)</a>, and the <a href="https://galaxyproject.org" target="_blank">Galaxy project</a>.
The service is part of the European Galaxy server and is maintained by the <a href="https://www.denbi.de/network/rna-bioinformatics-center-rbc" target="_blank">RNA Bioinformatics Center (RBC)</a> as part of <a href="https://www.denbi.de" target="_blank">de.NBI</a> and <a href="http://elixir-europe.org" target="_blank">ELIXIR</a>.</p>
<div align="center">
<table border="0">
<tr>
<td with="10%"></td>
<td width="20%">
<img alt="VGP" src="/assets/media/vgp_logo.png" />
</td>
<td with="40%"></td>
<td width="16%">
<img alt="ERGA" src="/assets/media/erga_logo.png" />
</td>
<td with="40%"></td>
<td width="20%">
<img alt="HPRC" src="/assets/media/hprc_logo.png" />
</td>
<td with="10%"></td>
</tr>
</table>
</div>
<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>
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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
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(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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