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<!doctype html>
<html lang="en">
<head>
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<script async src="https://www.googletagmanager.com/gtag/js?id=UA-118990564-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-118990564-1');
</script>
<meta charset="utf-8" name="viewport" content="width=device-width, initial-scale=1.0">
<title>SequencEnG</title>
<!-- Latest compiled and minified CSS -->
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<link rel="stylesheet" href="./css/keen-dashboards.css">
<link rel="stylesheet" href="./css/style.css">
</head>
<body class="application">
<div id="header">
</div>
<div id="other">
</div>
<div class="main-home container-fluid">
<div class="container-fluid">
<div class="tree-field">
<div class="row tree-intro tree-field-buttons">
<div class="col-12 col-sm-12 col-md-4" data-step="1" data-intro= "Welcome to SequencEnG, an interactive learning resource for NGS. <br>• Expand the whole knowledge tree to 68 major next-generation sequencing (NGS) techniques up to date. <br> • Collapse the tree to view 28 categories and learn about what biological information NGS techniques can measure.<br> • Search and select an NGS technique. <br> • Clear search first, if you want to search for another NGS technique.">
<div class="container">
<div class="chart-wrapper util-buttons">
<div class="chart-title">
Sequencing Tree
</div>
<div class="row justify-content-center">
<div class="col-md-6">
<button id="expand-all" class="btn btn-outline-success">
Expand All
</button>
</div>
<div class="col-md-6">
<button id="collapse-all" class="btn btn-outline-success">
Collapse All
</button>
</div>
</div>
<div class="row justify-content-center">
<div class="col-md-6">
<select id="search" >
<option></option>
</select>
</div>
<div class="col-md-6">
<button id="clear-all" class="btn btn-outline-info">
Clear Search
</button>
</div>
</div>
</div>
</div>
</div>
<div class="col-12 col-sm-12 col-md-6" data-step="12" data-intro="If you want to access the pipelines directly, choose one of the 13 pipelines from the dropdown lists. ">
<div class="container">
<div class="chart-wrapper analysis-pipeline">
<div class="chart-title">
Analysis Pipelines
</div>
<div class="row justify-content-center">
<div class="dropdown col-md-4">
<button class="btn btn-success dropdown-toggle" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
DNA
</button>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" data-seqname='WGS' href="#">WGS</a>
<a class="dropdown-item" data-seqname='WES' href="#">WES</a>
</div>
</div>
<div class="dropdown col-md-4">
<button class="btn btn-success dropdown-toggle" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
RNA
</button>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" data-seqname='RNA-seq' href="#">RNA-seq</a>
<a class="dropdown-item" data-seqname='scRNA-seq' href="#">scRNA-seq</a>
<a class="dropdown-item" data-seqname='CLIP-seq' href="#">CLIP-seq</a>
</div>
</div>
<div class="dropdown col-md-4">
<button class="btn btn-success dropdown-toggle" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Epigenetics
</button>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" data-seqname='TF_ChIP-seq' href="#">TF ChIP-seq</a>
<a class="dropdown-item" data-seqname='Histone_ChIP-seq' href="#">Histone ChIP-seq</a>
<a class="dropdown-item" data-seqname='Hi-C' href="#">Hi-C</a>
<a class="dropdown-item" data-seqname='ChIA-PET' href="#">ChIA-PET</a>
<a class="dropdown-item" data-seqname='DNase-seq' href="#">DNase-seq</a>
<a class="dropdown-item" data-seqname='ATAC-seq' href="#">ATAC-seq</a>
<a class="dropdown-item" data-seqname='WGBS' href="#">Bisulfite Sequencing</a>
<a class="dropdown-item" data-seqname='MNase-seq' href="#">MNase-seq</a>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row tree-info">
<div class="col-md-6">
<p>For optimal performance, please use Chrome, Firefox or Safari non-private mode.</p>
<p>Interactive analysis pipelines are available for sequencing techniques with "*".</p>
</div>
</div>
<div class="row tree-container">
<div class="tree-intro col-12 col-sm-12 col-md-7 col-lg-7 col-xl-8" id="tree" data-step="2" data-intro="The SequencEnG knowledgetree of current major NGS techniques, grouped by general and detailed categories."></div>
<div class="col-12 col-sm-12 col-md-4 col-lg-4 col-xl-4" id="desc" >
</div>
</div>
</div>
</div>
<div id="main" class="container-fluid" data-step="9" data-intro='After clicking the "Analysis pipeline" button, the NGS data analysis flow chart shows here.' >
<div class="row">
<div class="col-sm-12">
<div class="chart-wrapper">
<div class="chart-title">
Overview
</div>
<div class="chart-stage">
<div class="container-fluid">
<div class="row">
<div class="col-md-4">
<button id="chart-button" type="button" class="btn btn-outline-success">Show analysis flow chart</button>
</div>
<div class="col-md-4">
<button id="tree-button" type="button" class="btn btn-outline-success">Go to SequencEnG Tree</button>
</div>
</div>
</div>
</div>
<div class="chart-notes">
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-12">
<div class="chart-wrapper">
<div class="chart-title pipeline-title">
Flow Chart
</div>
<div class="chart-stage">
<div class="chart-container container-fluid" >
<div class="row justify-content-center chart-row">
<div data-step="10" data-intro="Click on the analysis steps to view sub-steps and software/tools available in the next section." class="col-10 col-md-10" id="flowchart-wrapper">
<div id="svgContainer">
<svg id="svg-pipe" width="0" height="0" >
</svg>
</div>
<div id="chart" class="container-fluid">
</div>
</div>
</div>
</div>
</div>
<div class="chart-notes">
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-sm-12">
<div class="chart-wrapper">
<div class="chart-title">
Table
</div>
<div class="chart-stage">
<div class="container">
<div data-step="11" data-intro="Each row is a popular software/tool for the current analysis step; Features and comparison among tools are shown. Scroll right to see more columns to see more features and links." class="row justify-content-center table-row">
<div class="container table-info-text">
</div>
<table id="table" class="display cell-border hover" cellspacing="0" width="100%">
</table>
</div>
</div>
</div>
<div class="chart-notes">
</div>
</div>
</div>
</div>
</div>
</div>
<div id="footer"></div>
<!-- The Modal -->
<div id="modalbox" class="modal">
<span class="modalclose">×</span>
<img class="modal-content" id="img-modal">
<div id="caption"></div>
</div>
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