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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="description" content="A front-end template that helps you build fast, modern mobile web apps.">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>COSMOS</title>
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rel="stylesheet">
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<link rel="stylesheet" href="styles.css">
<style>
#view-source {
position: fixed;
display: block;
right: 0;
bottom: 0;
margin-right: 40px;
margin-bottom: 40px;
z-index: 900;
}
</style>
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<a href="#Overview" class="mdl-layout__tab is-active">Overview</a>
<a href="#Cite" class="mdl-layout__tab is-active">Cite</a>
<a href="#Code" class="mdl-layout__tab">Download</a>
<a href="#Documentation" class="mdl-layout__tab is-active">Documentation</a>
<a href="#Publications" class="mdl-layout__tab is-active">Publications</a>
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<a href="#Publications" class="mdl-layout__tab is-active">Publications</a>
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<h4>COSMOS: Workflow Management System</h4>
<p><strong>COSMOS</strong> is a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user-interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. It is developed jointly by the <a href="http://lpm.hms.harvard.edu">Laboratory for Personalized Medicine</a> at Harvard Medical School, <a href="http://invitae.com">Invitae</a>, a clinical next generation sequencing diagnostic laboratory, and the <a href="http://wall-lab.stanford.edu/">Wall Lab</a> at Stanford University.</p>
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<a href="http://bioinformatics.oxfordjournals.org/content/30/20/2956.full?sid=12dd5c01-fc2b-4d78-80cc-eed064039844" target="_blank" class="mdl-button">Read the Bioinformatics application note</a>
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<h4>How to Cite COSMOS</h4>
<table>
<tr>
<th></th>
<th></th>
</tr>
<tr>
<td><p>Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung J-Y, Souilmi Y, Wall DP, Tonellato PJ: COSMOS: Python library for massively parallel workflows. Bioinformatics (2014) 30 (20): 2956-2958. <a href="http://bioinformatics.oxfordjournals.org/content/30/20/2956.full?sid=12dd5c01-fc2b-4d78-80cc-eed064039844" target="_blank">doi: 10.1093/bioinformatics/btu385</a></p></td>
<td><div data-badge-popover="right" data-badge-type="medium-donut" data-doi="10.1093/bioinformatics/btu385 e.2014.14583" class="altmetric-embed"></div></td>
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<a href="Cite_COSMOS.bib" target="_blank" class="mdl-button">Download formated citation</a>
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</div>
</section>
<!-- DOWNLOADS -->
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<div class="mdl-card mdl-cell mdl-cell--12-col">
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<h4 class="mdl-cell mdl-cell--12-col">Download COSMOS Code</h4>
<h6>COSMOS is avaialable in two versions:</h6><br>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>COSMOS 2.0</strong></h5>
<p>COSMOS 2.0 is production ready and available for <a href="https://github.com/Mizzou-CBMI/COSMOS2" target="_blank">download</a> fully open source under an MIT license</p>
COSMOS 2.0 code is available on gihtub as well as through Python PIP repository.</p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>COSMOS 1.0</strong> <i>(deprecated)</i></h5>
<p>COSMOS 1.0 is available for <a href="download.html" target="_blank">download</a> FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES.</p>
</div>
</div>
</section>
<!-- Documentation -->
<section id="Documentation" class="section--center mdl-grid mdl-grid--no-spacing mdl-shadow--2dp">
<div class="mdl-card mdl-cell mdl-cell--12-col">
<div class="mdl-card__supporting-text mdl-grid mdl-grid--no-spacing">
<h4 class="mdl-cell mdl-cell--12-col">COSMOS Documentation</h4>
<h6>COSMOS documentations for the version 1.0 and 2.0 are available:</h6><br>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>COSMOS 2.0</strong></h5>
<p>COSMOS 2.0 release documentation is available to build from the code, and also accessible online here:
<a href="http://Mizzou-CBMI.github.io/COSMOS2/" target="_blank">Access online documentation</a></p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>COSMOS 1.0</strong> <i>(deprecated)</i></h5>
<p>COSMOS 1.0 documentation is available to build from the code, and also accessible here:
<a href="http://Mizzou-CBMI.github.io/COSMOS2/" target="_blank">Access online documentation</a></p>
</div>
</div>
<div class="mdl-card__actions">
<a href="https://gitter.im/LPM-HMS/Cosmos2?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge" target="_blank" class="mdl-button" rel="nofollow">Contact us on the support room: <img src="https://badges.gitter.im/Join%20Chat.svg"></a>
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</section>
<!-- Publications -->
<section id="Publications" class="section--center mdl-grid mdl-grid--no-spacing mdl-shadow--2dp">
<div class="mdl-card mdl-cell mdl-cell--12-col">
<div class="mdl-card__supporting-text mdl-grid mdl-grid--no-spacing">
<h4 class="mdl-cell mdl-cell--12-col">COSMOS Publications</h4>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone" id="bench2">
<h5><strong>BMC Medical Genomics</strong></h5>
<p>Souilmi Y., Lancaster AK, Jung J-Y., Ettore R., Jared HB., Ryan Powles, Amzazi S., Ghazal H., Tonellato, P., Wall DP. (2015). Scalable and Cost-effective NGS Genotyping in the Cloud. Forthcoming.</p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone" id="bench1">
<h5><strong>BMC Bioinformatics: ISCB Student Council Symposium 2014 Highlight</strong></h5>
<p>Souilmi Y., Jung J-Y., Lancaster AK, Gafni E., Amzazi S., Ghazal H., Wall DP., Tonellato, P. (2015). COSMOS: cloud enabled NGS analysis. BMC Bioinformatics, 16(Suppl 2), A2. <a href="http://www.biomedcentral.com/1471-2105/16/S2/A2" target="_blank">doi: 10.1186/1471-2105-16-S2-A2</a></p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Bioinformatics Application Note</strong></h5>
<p>Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung J-Y, Souilmi Y, Wall DP, Tonellato PJ: COSMOS: Python library for massively parallel workflows. Bioinformatics (2014) 30 (20): 2956-2958. <a href="http://bioinformatics.oxfordjournals.org/content/30/20/2956.full?sid=12dd5c01-fc2b-4d78-80cc-eed064039844" target="_blank">doi: 10.1093/bioinformatics/btu385</a></p>
</div>
</div>
</section>
<!-- Workflows -->
<section id="Workflows" class="section--center mdl-grid mdl-grid--no-spacing mdl-shadow--2dp">
<div class="mdl-card mdl-cell mdl-cell--12-col">
<div class="mdl-card__supporting-text mdl-grid mdl-grid--no-spacing">
<h4 class="mdl-cell mdl-cell--12-col">COSMOS Compatible Workflows</h4>
We share here COSMOS compatible workflows:
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>GenomeKey</strong></h5>
<p>GenomeKey 1.0 is a COSMOS 1.0 implementation of GATK best practices. It offers high-performance and high-throughput whole exome/genome data analysis. GenomeKey's performance was systematically benchmarked as shown in <a href="#bench1" target="_blank">the BMC Bioinformatics preview</a> and <a href="#bench2" target="_blank">the full BMC Medical Genomics paper</a>.</p>
<p>GenomeKey 1.0 is <a href="https://github.com/Mizzou-CBMI/GenomeKey" target="_blank">available</a> under APACHE 2.0 LICENCE.</p>
<p><strong>Note 1</strong>: We are also building a COSMOS 2.0 compatible version.
<br><strong>Note 2</strong>: For instructions on how to use Genomekey on AWS, please refer to the github <a href="https://github.com/Mizzou-CBMI/GenomeKey/wiki/COSMOS-and-Genomekey-on-AWS" target="_blank">wiki page</a>. </p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>PvKey</strong></h5>
<p>PvKey 1.0 is a COSMOS 1.0 workflow for Tumor-Normal matched samples analysis. It calls somatic variants using Mutect and structural variants using SVDetect. It can handle genome, exome and targeted samples (TruSeq Custom Amplicon).</p>
<p>PvKey 1.0 is <a href="https://github.com/Mizzou-CBMI/PvKey" target="_blank">available</a> under APACHE 2.0 LICENCE.</p>
<p><strong>Note 1</strong>: We are also building a COSMOS 2.0 compatible version.
<br><strong>Note 2</strong>: For instructions on how to use PvKey, please refer to the github <a href="https://github.com/Mizzou-CBMI/PvKey/blob/master/README.md" target="_blank">instructions page</a>. </p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Where can I find documentation?</strong></h5>
<p>You can refer to the <a href="#Documentation">documentation section</a> for more details.</p>
</div>
</div>
</section>
<!-- FAQ -->
<section id="FAQ" class="section--center mdl-grid mdl-grid--no-spacing mdl-shadow--2dp">
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<h4 class="mdl-cell mdl-cell--12-col">FAQ</h4>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Is COSMOS free to use?</strong></h5>
<p>COSMOS is available in two versions 1.0 and 2.0. Version 1.0 is free and open FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES only, please check the <a href="download.html#License" target="_blank">license agreement</a>. COSMOS 2.0 is production ready, open source and available under MIT LICENCE.</p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>How can I get COSMOS?</strong></h5>
<p>You can refer to the <a href="#Code">download section</a> for more details.</p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Where can I find documentation?</strong></h5>
<p>You can refer to the <a href="#Documentation">documentation section</a> for more details.</p>
</div>
<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Where can I find support?</strong></h5>
<p>You use the Please use the <a href="https://github.com/Mizzou-CBMI/Cosmos2/issues" target="_blank">Github Issue Tracker</a>, or contact us on the support room: <a href="https://gitter.im/LPM-HMS/Cosmos2?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge" rel="nofollow"><img src="https://badges.gitter.im/Join%20Chat.svg"></a></p>
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<div class="section__text mdl-cell mdl-cell--10-col-desktop mdl-cell--6-col-tablet mdl-cell--3-col-phone">
<h5><strong>Is COSMOS 2.0 compatible with 1.0's workflows?</strong></h5>
<p>COSMOS 2.0 was built with the same philosophy and keeps the same feature and adds many more. The new API was built using modern technics and is not backwards-compatible with 1.0 pipelines. However, the porting is not very complicated once you familiarize yourself with the new syntax, which is more self explenatory. Please refer to <a href="http://Mizzou-CBMI.github.io/COSMOS2/" target="_blank">Access online documentation</a> for more details.</p>
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