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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>QIIME 2</title>
<link rel="stylesheet" href="./assets/css/normalize.css" media="screen">
<link rel="stylesheet" href="./assets/css/bootstrap.min.css" media="screen">
<link rel="stylesheet" href="./assets/css/main.css" media="screen">
<link rel="icon" href="./assets/favicon.ico" type="image/png" />
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-86671044-1', 'auto');
ga('send', 'pageview');
</script>
</head>
<body>
<nav class="navbar navbar-default navbar-fixed-top">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li class="active"><a href="https://qiime2.org">Home</a></li>
<li><a href="https://library.qiime2.org">Library</a></li>
<li><a href="https://docs.qiime2.org">Docs</a></li>
<li><a href="https://forum.qiime2.org">Forum</a></li>
<li><a href="https://workshops.qiime2.org">Workshops</a></li>
<li><a href="https://view.qiime2.org">View</a></li>
</ul>
</div>
</div>
</nav>
<div class="jumbotron">
<div class="container">
<div class="row">
<div class="col-md-4">
<img class="img-responsive" src="./assets/img/qiime2.svg">
</div>
<div class="col-md-8">
<p>
QIIME 2™ is a next-generation microbiome bioinformatics platform
that is extensible, free, open source, and <a href="https://github.com/orgs/qiime2/people" target="_blank">community developed.</a>
</p>
<p>
<a class="btn btn-info btn-lg" href="https://github.com/qiime2/.github/blob/main/CODE-OF-CONDUCT.md" role="button">Code of Conduct »</a>
<a class="btn btn-success btn-lg" href="#citing" role="button">Citing QIIME 2 »</a>
<a class="btn btn-primary btn-lg" href="https://docs.qiime2.org" role="button">Learn more »</a>
</p>
</div>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="col-md-3">
<img class="img-responsive center-block bottom-pad" width="100" height="100" src="./assets/img/provenance.svg">
<p class="text-justify">Automatically track your analyses with
decentralized data provenance — no more guesswork on what commands were
run!</p>
</div>
<div class="col-md-3">
<img class="img-responsive center-block bottom-pad" width="100" height="100" src="./assets/img/viz.svg">
<p class="text-justify">Interactively explore your data with beautiful
visualizations that provide new perspectives.</p>
</div>
<div class="col-md-3">
<img class="img-responsive center-block bottom-pad" width="100" height="100" src="./assets/img/sharing.svg">
<p class="text-justify">Easily share results with your team, even those
members without QIIME 2 installed.</p>
</div>
<div class="col-md-3">
<img class="img-responsive center-block bottom-pad" width="100" height="100" src="./assets/img/plugin.svg">
<p class="text-justify">Plugin-based system — your favorite microbiome methods all in one place.</p>
</div>
</div>
<hr>
<div>
<h3 id="interfaces" class="trim-the-top-margin">Choose the interface that fits your needs</h3>
<div class="row">
<div class="col-md-4">
<div class="row bottom-pad">
<div class="col-md-12">
<h4>
<a href="https://docs.qiime2.org/2024.5/interfaces/q2cli/">q2cli</a>
<small>the command line interface</small>
</h4>
<img class="img-responsive center-block interface" src="./assets/img/q2cli.png">
</div>
</div>
<div class="row">
<div class="col-md-12">
<h4>
<a href="https://docs.qiime2.org/2024.5/interfaces/artifact-api/">Artifact API</a>
<small>the data scientist's interface</small>
</h4>
<img class="img-responsive center-block interface" src="./assets/img/artifact-api.png">
</div>
</div>
</div>
<div class="col-md-8">
<h4>
<a>q2galaxy</a>
<small>the graphical user interface</small>
</h4>
<img class="img-responsive center-block interface" src="./assets/img/q2galaxy.png">
</div>
</div>
</div>
<hr>
<div>
<h3 id="citing">Citing QIIME 2</h3>
<p>
If you use QIIME 2 for any published research, please include the
following citation:
</p>
<p class="well">
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA,
Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE,
Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ,
Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C,
Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF,
Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL,
Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H,
Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD,
Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I,
Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E,
Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ,
Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT,
Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL,
Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS,
Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ,
Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A,
Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y,
Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC,
Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q,
Knight R, and Caporaso JG. 2019. Reproducible, interactive, scalable
and extensible microbiome data science using QIIME 2.
<emph>Nature Biotechnology</emph> 37: 852–857.
<a href="https://doi.org/10.1038/s41587-019-0209-9">
https://doi.org/10.1038/s41587-019-0209-9
</a>
</p>
<p>
QIIME 2 plugins frequently utilize other software packages that
must be cited in addition to QIIME 2 itself. Run
<code>qiime tools citations</code>
on an Artifact or Visualization to discover all of the
citations relevant to the creation of that result. Lists of citations are provided by
<a href="https://view.qiime2.org">https://view.qiime2.org</a>
as well. To generate the list of citations for a QIIME 2 Artifact or Visualization,
navigate to the "Provenance" page, and then to the "Citations" tab.
</p>
</div>
<hr>
<footer>
<p>© 2016-2024, QIIME 2 development team</p>
</footer>
</div>
<script src="./assets/js/jquery.min.js"></script>
<script src="./assets/js/bootstrap.min.js"></script>
</body>
</html>