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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
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<meta name="description" content="The European Galaxy Instance">
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<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><img src="/assets/media/microgalaxy-logo.png" alt="microGalaxy logo" class="sc-intro-left" /></p>
<h1 id="welcome-to-microgalaxy">Welcome to microGalaxy!</h1>
<p class="no_toc"><br />
Whether you are analysing microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics, transcriptomics, proteomics or metabolomics, multiomics or integrative analysis <strong>this is the place to be</strong>!</p>
<p><br /></p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#welcome-to-microgalaxy" id="markdown-toc-welcome-to-microgalaxy">Welcome to microGalaxy!</a></li>
<li><a href="#join-the-μgalaxy-community" id="markdown-toc-join-the-μgalaxy-community">Join the μGalaxy Community</a></li>
<li><a href="#training" id="markdown-toc-training">Training</a> <ol>
<li><a href="#galaxy-training-network-tutorials-tagged-with-microgalaxy" id="markdown-toc-galaxy-training-network-tutorials-tagged-with-microgalaxy">Galaxy Training Network Tutorials tagged with <strong>#microGalaxy</strong></a></li>
</ol>
</li>
<li><a href="#workflows" id="markdown-toc-workflows">Workflows</a> <ol>
<li><a href="#microgalaxy-workflows" id="markdown-toc-microgalaxy-workflows">MicroGalaxy Workflows</a></li>
</ol>
</li>
<li><a href="#tools" id="markdown-toc-tools">Tools</a> <ol>
<li><a href="#curated-community-tool-list" id="markdown-toc-curated-community-tool-list">Curated community tool list</a></li>
</ol>
</li>
<li><a href="#projects" id="markdown-toc-projects">Projects</a> <ol>
<li><a href="#projects--showcases" id="markdown-toc-projects--showcases">Projects / Showcases</a></li>
<li><a href="#partners" id="markdown-toc-partners">Partners</a></li>
</ol>
</li>
<li><a href="#resources" id="markdown-toc-resources">Resources</a></li>
</ol>
<h1 id="join-the-μgalaxy-community">Join the μGalaxy Community</h1>
<p>Anybody interested in microbiology in Galaxy is welcome to join our microGalaxy interest group! <strong>Everybody is Welcome!</strong></p>
<ul>
<li>Join the Discussion! <a href="https://gitter.im/galaxyproject/microGalaxy">Gitter Chat</a> (also available via <a href="https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im">Matrix</a>)</li>
<li>Join our quarterly meetings! <a href="https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEWr254/edit#">Agenda and minutes</a></li>
</ul>
<h1 id="training">Training</h1>
<p>Want to learn even more about microbial analysis? You can check out our various microbial dedicated training page within the wider Galaxy Training Network.</p>
<ul>
<li><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/learning-pathways/metagenomics.html\">Metagenomic learning paths</a></li>
<li><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/topics/metabolomics/">Metabolomics</a></li>
<li><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/topics/genome-annotation/">Genome Annotation</a></li>
<li><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/topics/evolution/">Tuberculosis evolution</a></li>
<li><i class="fa fa-book" aria-hidden="true"></i> <a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/">Microbial Variant Calling</a></li>
</ul>
<h2 id="galaxy-training-network-tutorials-tagged-with-microgalaxy">Galaxy Training Network Tutorials tagged with <strong>#microGalaxy</strong></h2>
<!-- tag all trainings with microGalaxy and update the link -->
<iframe src="https://training.galaxyproject.org/training-material/tags/microgalaxy/embed.html" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>
<h1 id="workflows">Workflows</h1>
<p>Below are a list of curated Galaxy workflows for different kinds of microbial analysis. Many of these are accompanied by comprehensive <a href="https://training.galaxyproject.org">GTN Tutorials</a> that will guide you through the analysis step by step.
Want to include your workflow here? All you need to do is to make your workflow publicly available via <code class="highlighter-rouge">usegalaxy.eu/.org/.org.au.</code> (or any of the subdomains) and tag the workflow with <strong>#microGalaxy</strong>.</p>
<h2 id="microgalaxy-workflows">MicroGalaxy Workflows</h2>
<iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?query=microgalaxy" height="600px" width="100%" class="gtn-embed" frameborder="0"></iframe>
<h1 id="tools">Tools</h1>
<p>More than <strong>200 tools</strong> are available for microbiome data analysis in this custom Galaxy instance, major tools to highlight are:</p>
<ul>
<li><strong>General tools</strong>
<ul>
<li><strong>Data retrieval</strong>: EBISearch, ENASearch, SRA Tools</li>
<li><strong>BAM/SAM file manipulation</strong>: SAM tools</li>
<li><strong>BIOM file manipulation</strong>: BIOM-Format tools</li>
</ul>
</li>
<li><strong>Genomics tools</strong>
<ul>
<li><strong>Quality control</strong>: FastQC, PRINSEQ, Cutadapt, fastp, Trimmomatic, MultiQC</li>
<li><strong>Clustering</strong>: CD-Hit</li>
<li><strong>Sorting and prediction</strong>: SortMeRNA, FragGeneScan</li>
<li><strong>Mapping</strong>: BWA, Bowtie</li>
<li><strong>Similarity search</strong>: NCBI Blast+, Diamond</li>
<li><strong>Alignment</strong>: HMMER3</li>
</ul>
</li>
<li><strong>Microbiota dedicated tools</strong>
<ul>
<li><strong>Microbial</strong>: Scoary, Prokka, Roary</li>
<li><strong>Metagenomics data manipulation</strong>: VSearch, Nonpareil, DADA2</li>
<li><strong>Assembly</strong>: MEGAHIT, metaSPAdes, metaQUAST, VALET, Bandage, MaxBin2</li>
<li><strong>Metataxonomic sequence analysis</strong>: Mothur, QIIME, Vegan</li>
<li><strong>Taxonomy assignation</strong>: MetaPhlAn, Kraken, CAT/BAT</li>
<li><strong>Metabolism assignation</strong>: HUMAnN, PICRUST, InterProScan</li>
<li><strong>Visualization</strong>: Export2graphlan, GraPhlAn, KRONA</li>
<li><strong>Metaproteomics</strong>: MaxQuant, SearchGUI, PeptideShaker, Unipept</li>
</ul>
</li>
</ul>
<h2 id="curated-community-tool-list">Curated community tool list</h2>
<p>The complete curated list of all the tools is weekly updated and available here:</p>
<iframe id="inlineFrameExample" title="Microbial related tools" width="100%" height="600" frameborder="0" src="https://galaxyproject.github.io/galaxy_codex/microgalaxy/">
</iframe>
<p>Want to know how this list is created and maintained have a look at the dedicated <a href="https://github.com/galaxyproject/galaxy_codex">GitHub project</a>. If tools are missing or information is not up-to-date in the list, please help us! Contact Saskia, <a href="mailto:zierep@informatik.uni-freiburg.de">Paul</a> or <a href="mailto:berenice.batut@gmail.com">Bérénice</a> about it.</p>
<h1 id="projects">Projects</h1>
<p>Below is a list of projects that members of this community are involved in (feel free to add your own!)</p>
<h2 id="projects--showcases">Projects / Showcases</h2>
<p>Below is a list of projects involving members of this community:</p>
<table class="table table-striped">
<thead>
<tr>
<th>Project</th>
<th>Description</th>
<th>Techniques</th>
<th>Sequencing</th>
<th>Analyses</th>
<th>People involved</th>
<th>Funding</th>
<th>Status</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://irida.ca/">IRIDA</a></td>
<td>The Integrated Rapid Infectious Disease Analysis</td>
<td> </td>
<td> </td>
<td> </td>
<td>Aaron Petkau</td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>Foodborne pathogen detection</td>
<td> </td>
<td>Metagenomics</td>
<td>Long reads</td>
<td> </td>
<td>Bérénice Batut, Engy Nasr</td>
<td>EOSC-Life for 2022</td>
<td>Ongoing</td>
</tr>
<tr>
<td><a href="https://streetscience.community/projects/beerdecoded/">BeerDEcoded</a></td>
<td>General public education project</td>
<td>Metagenomics</td>
<td>Long reads</td>
<td> </td>
<td>Bérénice Batut, <a href="https://streetscience.community/">Street Science Community</a></td>
<td>Mozilla, de.NBI</td>
<td>Ongoing</td>
</tr>
<tr>
<td><a href="http://streetscience.community/DNAnalyzer/">DNAnalyzer</a></td>
<td>Online & interactive game on DNA data analysis</td>
<td>Metagenomics</td>
<td>Long reads</td>
<td> </td>
<td>Bérénice Batut, <a href="https://streetscience.community/">Street Science Community</a></td>
<td>University of Freiburg</td>
<td>Ongoing</td>
</tr>
<tr>
<td>Cloud data</td>
<td> </td>
<td>Metagenomics, metatranscriptomics</td>
<td>Short reads</td>
<td>Taxonomy profiling, Functional profiling, Assembly, MAGs builiding</td>
<td>Bérénice Batut, Engy Nasr</td>
<td> </td>
<td>Ongoing</td>
</tr>
<tr>
<td>ASaiM</td>
<td> </td>
<td>Metagenomics, metatranscriptomics</td>
<td>Short reads</td>
<td>Taxonomy profiling, Functional profiling</td>
<td>Bérénice Batut, Saskia Hilteman, Pratik Jagtap, Subina Mehta, etc</td>
<td> </td>
<td>Finished?</td>
</tr>
<tr>
<td><a href="https://gallantries.github.io/video-library/modules/mtb-analysis">Mycobacterium tuberculosis NGS made easy: data</a></td>
<td>Series of modules containing recorded videos by experts and tutorials</td>
<td> </td>
<td>Illumina (wanting to expand to nanopore)</td>
<td>Mapping & Variant calling, Molecular epidemiology of TB using NGS, Phylogenetics for studying TB evolution and epidemiology</td>
<td>Daniela Brites, Peter van Heusden, Galo A. Goig, Christoph Stritt</td>
<td>Initially funded trough TB projects of capacity building; currently no funding</td>
<td>Ready to be used but also working on improvements</td>
</tr>
</tbody>
</table>
<h2 id="partners">Partners</h2>
<table class="table table-striped">
<thead>
<tr>
<th>Partners</th>
<th>Description</th>
<th>People involved</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://www.jpiamr.eu/projects/seq4amr/">Seq4AMR</a></td>
<td><a href="">JPIAMR</a> Network for Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance</td>
<td>Saskia Hilteman</td>
</tr>
<tr>
<td><a href="https://elixir-europe.org/communities/marine-metagenomics">ELIXIR Emerging Microbiome Community</a></td>
<td> </td>
<td>Bérénice Batut</td>
</tr>
<tr>
<td>µbioinfo Slack</td>
<td> </td>
<td><a href="https://microbial-bioinfo.slack.com">microbial-bioinfo</a></td>
</tr>
</tbody>
</table>
<p>If you would like to know more about any of these projects or get involved, please contact us on the <a href="https://gitter.im/galaxyproject/microGalaxy">microGalaxy Gitter channel</a>.</p>
<h1 id="resources">Resources</h1>
<table class="table table-striped">
<thead>
<tr>
<th>Resource</th>
<th>Description</th>
<th>Links</th>
</tr>
</thead>
<tbody>
<tr>
<td><img src="https://www.jpiamr.eu/app/uploads/2021/09/JPIAMR-logo-no-tagline.png" alt="" width="100px" /></td>
<td>JPIAMR: Global Coordination of Antimicrobial Resistance Research</td>
<td><a href="https://www.jpiamr.eu/">Website</a></td>
</tr>
</tbody>
</table>
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