195 lines
7.7 KiB
HTML
195 lines
7.7 KiB
HTML
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<!DOCTYPE html>
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<html lang="{{ site.language }}">
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<head>
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{% capture title %}{% if page.title %}{{ page.title }} | {% endif %}{{ site.title }}{% endcapture %}
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{% include page-url-resolver.html page=page %}
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{% if page.excerpt %}
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{% assign description = page.excerpt | strip_html | strip_newlines | truncate: 160 %}
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{% else %}
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{% assign description = site.description %}
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{% endif %}
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>{{ title }}</title>
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<meta name="description" content="{{ description }}">
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<link rel="shortcut icon" href="{{ site.favicon | prepend: site.baseurl }}" type="image/x-icon">
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<link rel="canonical" href="{{ url }}">
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<link rel="alternate" type="application/atom+xml" title="{{ site.title }}" href="{{ '/feed.xml' | prepend: site.baseurl }}" />
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{% if page.eye_catch %}
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{% assign ogp_image_url = page.eye_catch %}
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{% else %}
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{% assign ogp_image_url = site.ogp.image_url %}
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{% endif %}
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<meta property="og:title" content="{{ title }}" />
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<meta property="og:type" content="website" />
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<meta property="og:image" content="{{ ogp_image_url }}" />
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<meta property="og:url" content="{{ url }}" />
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<meta property="og:site_name" content="{{ site.title }}" />
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<meta property="fb:admins" content="{{ site.ogp.fb.admin }}" />
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<meta property="fb:app_id" content="{{ site.ogp.fb.app_id }}" />
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<meta property="og:description" content="{{ description }}" />
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<!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]-->
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<script src="https://use.fontawesome.com/1f5f360d80.js"></script>
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<link href="//fonts.googleapis.com/css?family=Source+Sans+Pro:400,700,700italic,400italic" rel="stylesheet">
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<link href="{{ '/assets/css/style.css' | prepend: site.baseurl }}" rel="stylesheet">
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</head>
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<body>
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<header class="site-header">
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<div class="inner clearfix">
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{% if site.avatar %}
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<a href="{{ '/' | prepend: site.baseurl }}">
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<img class="avatar" src="{{ site.avatar | prepend: site.baseurl }}" alt=""/>
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</a>
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{% endif %}
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<h1 class="clearfix">
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<a class="title {% if site.avatar == null %}slim{% endif %}" href="{{ '/' | prepend: site.baseurl }}">{{ site.title }}</a>
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<br><span class="description">{{ site.description }}</span>
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</h1>
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</div>
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</header>
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<div class="site-container">
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<div class="site-content">
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{{ content }}
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</div>
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<aside class="site-aside">
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<div class="inner">
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<div class="block">
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<form action="{{ site.baseurl }}/search">
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<input type="search" id="search" name="q" placeholder="{{ site.str_search }}" />
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</form>
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</div>
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<div class="block">
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<ul>
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{% assign pages = site.pages | where: "category", "main" | sort: 'order' %}
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{% for page in pages %}
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{% if page.title and page.hide != true %}
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<li><a class="page-link" href="{{ page.url | prepend: site.baseurl }}">{{ page.title }}</a></li>
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{% endif %}
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{% endfor %}
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</ul>
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</div>
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<!--
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<ul class="icons">
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{% include icons.html icons=site.icons %}
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</ul>
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<hr class="with-no-margin margin-bottom"/>
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-->
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<div class="block">
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<h2>Funding</h2>
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<br>
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<div style="font-size: 0.8em">
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This work was supported in part by the National Human Genome Research Institute under grants R01-HG006102 and R01-HG006677,
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and NIH grants R01-LM06845 and R01-GM083873 and NSF grant CCF-0347992 to Steven L. Salzberg
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and by the Cancer Prevention Research Institute of Texas under grant RR170068 and NIH grant R01-GM135341 to Daehwan Kim
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</div>
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</div>
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<div class="block">
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<h2>Getting Help</h2>
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<br>
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Please use <a href="mailto:hisat2.genomics@gmail.com">hisat2.genomics@gmail.com</a> for private communications only. Please do not email technical questions to HISAT2 contributors directly.
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</div>
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<div class="block">
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<h2>Publications</h2>
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<div style="font-size: 0.8em">
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<ul>
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<li>Kim, D., Paggi, J.M., Park, C. <i>et al.</i> <a class="publication" href="https://doi.org/10.1038/s41587-019-0201-4">Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.</a> <a class="publication" href="https://www.nature.com/nbt/"><i>Nat Biotechnol</i></a> <b>37</b>, 907–915 (2019).</li>
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<li>Kim D, Langmead B and Salzberg SL. <a class="publication" href="https://doi.org/10.1038/nmeth.3317">HISAT: a fast spliced aligner with low memory requirements.</a> <a class="publication" href="https://www.nature.com/nmeth/"><i>Nature Methods</i></a> 2015</li>
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<li>Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. <a class="publication" href="https://doi.org/10.1038/nprot.2016.095">Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.</a> <a class="publication" href="https://www.nature.com/nprot/"><i>Nature Protocols</i></a> 2016</li>
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</ul>
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</div>
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</div>
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<div class="block">
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<h2>Contributors</h2>
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<ul>
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{% for item in site.data.contributor %}
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<li>
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{% if item.url contains "http://" or item.url contains "https://" %}
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<a class="page-link" href="{{ item.url }}">{{ item.name }}</a>
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{% else %}
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<a class="page-link" href="{{ item.url | prepend: site.baseurl }}">{{ item.name }}</a>
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{% endif %}
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</li>
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{% endfor %}
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</ul>
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</div>
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{% if site.data.collaborate %}
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<div class="block">
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{% for item in site.data.collaborate %}
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<ul style="text-align: center">
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<a href="{{ item.url }}">
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<img class="avatar" src="{{ item.logo | prepend: site.baseurl }}" alt="{{ item.name }}" />
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</a>
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</ul>
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{% endfor %}
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</div>
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{% endif %}
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<!--
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<div class="block sticky">
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<h2>{{ site.str_recent_posts }}</h2>
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<ul>
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{% assign posts = '' | split: '' %}
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{% for post in site.posts %}
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{% if post.hide != true %}
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{% assign posts = posts | push: post %}
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{% endif %}
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{% endfor %}
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{% assign posts = posts | sort: 'date' | reverse %}
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{% for post in posts limit:site.recent_posts_num %}
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<li><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a></li>
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{% endfor %}
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</ul>
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</div>
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-->
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</div>
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</aside>
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</div>
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<footer class="site-footer">
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<div class="inner">
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<span>Powered by <a href="http://jekyllrb.com">Jekyll</a> with <a href="https://github.com/ttskch/jekyll-ttskch-theme">TtskchTheme</a></span>
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</div>
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</footer>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
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<script src="{{ '/assets/lib/garand-sticky/jquery.sticky.js' | prepend: site.baseurl }}"></script>
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<script src="{{ '/assets/js/script.js' | prepend: site.baseurl }}"></script>
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{% if page.id %}
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<script src="{{ '/assets/js/header-link.js' | prepend: site.baseurl }}"></script>
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{% endif %}
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{% if page.permalink == '/search/' %}
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<script src="{{ '/assets/js/search.js' | prepend: site.baseurl }}"></script>
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{% endif %}
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{% include fb-root.html %}
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{% include google-analytics.html %}
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</body>
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</html>
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