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Unknown committed Jul 26, 2023
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6 changes: 3 additions & 3 deletions index.html
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Expand Up @@ -112,7 +112,7 @@ <h1 id="table-of-contents">Table of Contents</h1>
<li><a href="#documentation">Documentation</a></li>
<li><a href="#credits">Credits</a></li>
<li><a href="#contributing">Contributing to ARETE</a></li>
<li><a href="#citations">Citations</a></li>
<li><a href="#citing">Citing ARETE</a></li>
</ol>
<h2 id="about-the-pipeline">About the pipeline <a name="about"></a></h2>
<p>The pipeline is built using <a href="https://www.nextflow.io">Nextflow</a>, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible.
Expand Down Expand Up @@ -216,7 +216,7 @@ <h2 id="contributing-to-arete">Contributing to ARETE <a name="contributing"></a>
<!--If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).-->

<p>Thank you for your interest in contributing to ARETE. We are currently in the process of formalizing contribution guidelines. In the meantime, please feel free to open an issue describing your suggested changes.</p>
<h2 id="citations">Citations <a name="citations"></a></h2>
<h2 id="citing-arete">Citing ARETE <a name="citing"></a></h2>
<p>Please cite the tools used in your ARETE run: a comprehensive list can be found in the <a href="CITATIONS/"><code>CITATIONS.md</code></a> file.</p>
<p>An early version of ARETE was used for assembly and feature prediction in <a href="https://pubmed.ncbi.nlm.nih.gov/36129737/">the following paper</a>:
Sanderson H, Gray KL, Manuele A, Maguire F, Khan A, Liu C, Navanekere Rudrappa C, Nash JHE, Robertson J, Bessonov K, Oloni M, Alcock BP, Raphenya AR, McAllister TA, Peacock SJ, Raven KE, Gouliouris T, McArthur AG, Brinkman FSL, Fink RC, Zaheer R, Beiko RG. Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents. Microb Genom. 2022 Sep;8(9):mgen000880. doi: 10.1099/mgen.0.000880. PMID: 36129737; PMCID: PMC9676038.</p>
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