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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Intro</a><ul>
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<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data"><i class="fa fa-check"></i><b>1.1</b> Data</a></li>
<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#figures"><i class="fa fa-check"></i><b>1.2</b> Figures</a></li>
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<li class="chapter" data-level="2" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>2</b> Workflow</a><ul>
<li class="chapter" data-level="2.1" data-path="workflow.html"><a href="workflow.html#info"><i class="fa fa-check"></i><b>2.1</b> Info</a></li>
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<li class="chapter" data-level="3" data-path="figure-1.html"><a href="figure-1.html"><i class="fa fa-check"></i><b>3</b> Figure 1</a><ul>
<li class="chapter" data-level="3.1" data-path="figure-1.html"><a href="figure-1.html#summary"><i class="fa fa-check"></i><b>3.1</b> Summary</a></li>
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<li class="chapter" data-level="3.2" data-path="figure-1.html"><a href="figure-1.html#details-of-f1.r"><i class="fa fa-check"></i><b>3.2</b> Details of <code>F1.R</code></a><ul>
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<li class="chapter" data-level="3.2.1" data-path="figure-1.html"><a href="figure-1.html#fig.-1-a"><i class="fa fa-check"></i><b>3.2.1</b> Fig. 1 A)</a></li>
<li class="chapter" data-level="3.2.2" data-path="figure-1.html"><a href="figure-1.html#fig.-1-b"><i class="fa fa-check"></i><b>3.2.2</b> Fig. 1 B)</a></li>
<li class="chapter" data-level="3.2.3" data-path="figure-1.html"><a href="figure-1.html#fig.-1-c"><i class="fa fa-check"></i><b>3.2.3</b> Fig. 1 C)</a></li>
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<li class="chapter" data-level="3.2.4" data-path="figure-1.html"><a href="figure-1.html#fig-1-complete"><i class="fa fa-check"></i><b>3.2.4</b> Fig 1 (complete)</a></li>
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<li class="chapter" data-level="4" data-path="figure-2.html"><a href="figure-2.html"><i class="fa fa-check"></i><b>4</b> Figure 2</a><ul>
<li class="chapter" data-level="4.1" data-path="figure-2.html"><a href="figure-2.html#summary-1"><i class="fa fa-check"></i><b>4.1</b> Summary</a></li>
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<li class="chapter" data-level="4.2" data-path="figure-2.html"><a href="figure-2.html#details-of-f2.r"><i class="fa fa-check"></i><b>4.2</b> Details of <code>F2.R</code></a><ul>
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<li class="chapter" data-level="4.2.1" data-path="figure-2.html"><a href="figure-2.html#reading-in-data"><i class="fa fa-check"></i><b>4.2.1</b> Reading in Data</a></li>
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<li class="chapter" data-level="4.2.2" data-path="figure-2.html"><a href="figure-2.html#computing-99.98-fst-percentiles"><i class="fa fa-check"></i><b>4.2.2</b> Computing 99.98 <em>F<sub>ST</sub></em> percentiles</a></li>
<li class="chapter" data-level="4.2.3" data-path="figure-2.html"><a href="figure-2.html#plotting"><i class="fa fa-check"></i><b>4.2.3</b> Plotting</a></li>
<li class="chapter" data-level="4.2.4" data-path="figure-2.html"><a href="figure-2.html#composing-the-final-figure"><i class="fa fa-check"></i><b>4.2.4</b> Composing the final figure</a></li>
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<li class="chapter" data-level="5" data-path="figure-3.html"><a href="figure-3.html"><i class="fa fa-check"></i><b>5</b> Figure 3</a><ul>
<li class="chapter" data-level="5.1" data-path="figure-3.html"><a href="figure-3.html#summary-2"><i class="fa fa-check"></i><b>5.1</b> Summary</a></li>
<li class="chapter" data-level="5.2" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.r"><i class="fa fa-check"></i><b>5.2</b> Details of <code>F3.R</code></a></li>
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<li class="chapter" data-level="5.3" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.plot_fun.r"><i class="fa fa-check"></i><b>5.3</b> Details of <code>F3.plot_fun.R</code></a></li>
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<li class="chapter" data-level="6" data-path="figure-4.html"><a href="figure-4.html"><i class="fa fa-check"></i><b>6</b> Figure 4</a><ul>
<li class="chapter" data-level="6.1" data-path="figure-4.html"><a href="figure-4.html#summary-3"><i class="fa fa-check"></i><b>6.1</b> Summary</a></li>
<li class="chapter" data-level="6.2" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.r"><i class="fa fa-check"></i><b>6.2</b> Details of <code>F4.R</code></a></li>
<li class="chapter" data-level="6.3" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.functions.r"><i class="fa fa-check"></i><b>6.3</b> Details of <code>F4.functions.R</code></a></li>
<li class="chapter" data-level="6.4" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.genomewide_box.r"><i class="fa fa-check"></i><b>6.4</b> Details of <code>F4.genomeWide_box.R</code></a></li>
<li class="chapter" data-level="6.5" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.peakarea_box.r"><i class="fa fa-check"></i><b>6.5</b> Details of <code>F4.peakArea_box.R</code></a></li>
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<li class="chapter" data-level="7" data-path="supplementary-figure-01.html"><a href="supplementary-figure-01.html"><i class="fa fa-check"></i><b>7</b> Supplementary Figure 01</a><ul>
<li class="chapter" data-level="7.1" data-path="supplementary-figure-01.html"><a href="supplementary-figure-01.html#preparation"><i class="fa fa-check"></i><b>7.1</b> Preparation</a></li>
<li class="chapter" data-level="7.2" data-path="supplementary-figure-01.html"><a href="supplementary-figure-01.html#content-of-circos_figure.r"><i class="fa fa-check"></i><b>7.2</b> Content of circos_figure.R</a></li>
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<li class="chapter" data-level="8" data-path="supplementary-figure-02.html"><a href="supplementary-figure-02.html"><i class="fa fa-check"></i><b>8</b> Supplementary Figure 02</a><ul>
<li class="chapter" data-level="8.1" data-path="supplementary-figure-02.html"><a href="supplementary-figure-02.html#summary-4"><i class="fa fa-check"></i><b>8.1</b> Summary</a></li>
<li class="chapter" data-level="8.2" data-path="supplementary-figure-02.html"><a href="supplementary-figure-02.html#details-of-s02.r"><i class="fa fa-check"></i><b>8.2</b> Details of <code>S02.R</code></a></li>
<li class="chapter" data-level="8.3" data-path="supplementary-figure-02.html"><a href="supplementary-figure-02.html#details-of-s02.functions.r"><i class="fa fa-check"></i><b>8.3</b> Details of <code>S02.functions.R</code></a></li>
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<li class="chapter" data-level="9" data-path="supplementary-figure-03.html"><a href="supplementary-figure-03.html"><i class="fa fa-check"></i><b>9</b> Supplementary Figure 03</a><ul>
<li class="chapter" data-level="9.1" data-path="supplementary-figure-03.html"><a href="supplementary-figure-03.html#summary-5"><i class="fa fa-check"></i><b>9.1</b> Summary</a></li>
<li class="chapter" data-level="9.2" data-path="supplementary-figure-03.html"><a href="supplementary-figure-03.html#details-of-s03.r"><i class="fa fa-check"></i><b>9.2</b> Details of <code>S03.R</code></a></li>
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<li class="chapter" data-level="10" data-path="supplementary-figure-05.html"><a href="supplementary-figure-05.html"><i class="fa fa-check"></i><b>10</b> Supplementary Figure 05</a><ul>
<li class="chapter" data-level="10.1" data-path="supplementary-figure-05.html"><a href="supplementary-figure-05.html#summary-6"><i class="fa fa-check"></i><b>10.1</b> Summary</a></li>
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<li class="chapter" data-level="10.2" data-path="supplementary-figure-05.html"><a href="supplementary-figure-05.html#details-of-s05.r"><i class="fa fa-check"></i><b>10.2</b> Details of <code>S05.R</code></a></li>
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<li class="chapter" data-level="11" data-path="supplementary-figure-06.html"><a href="supplementary-figure-06.html"><i class="fa fa-check"></i><b>11</b> Supplementary Figure 06</a><ul>
<li class="chapter" data-level="11.1" data-path="supplementary-figure-06.html"><a href="supplementary-figure-06.html#summary-7"><i class="fa fa-check"></i><b>11.1</b> Summary</a></li>
<li class="chapter" data-level="11.2" data-path="supplementary-figure-06.html"><a href="supplementary-figure-06.html#details-of-s06.r"><i class="fa fa-check"></i><b>11.2</b> Details of <code>S06.R</code></a><ul>
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<li class="chapter" data-level="11.2.1" data-path="supplementary-figure-06.html"><a href="supplementary-figure-06.html#suppl.-fig.-06-a"><i class="fa fa-check"></i><b>11.2.1</b> Suppl. Fig. 06 A)</a></li>
<li class="chapter" data-level="11.2.2" data-path="supplementary-figure-06.html"><a href="supplementary-figure-06.html#suppl.-fig.-06-b"><i class="fa fa-check"></i><b>11.2.2</b> Suppl. Fig. 06 B)</a></li>
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<li class="chapter" data-level="12" data-path="supplementary-figure-07.html"><a href="supplementary-figure-07.html"><i class="fa fa-check"></i><b>12</b> Supplementary Figure 07</a><ul>
<li class="chapter" data-level="12.1" data-path="supplementary-figure-07.html"><a href="supplementary-figure-07.html#summary-8"><i class="fa fa-check"></i><b>12.1</b> Summary</a></li>
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<li class="chapter" data-level="12.2" data-path="supplementary-figure-07.html"><a href="supplementary-figure-07.html#details-of-s07.r"><i class="fa fa-check"></i><b>12.2</b> Details of <code>S07.R</code></a><ul>
<li class="chapter" data-level="12.2.1" data-path="supplementary-figure-07.html"><a href="supplementary-figure-07.html#reading-in-data-1"><i class="fa fa-check"></i><b>12.2.1</b> Reading in Data</a></li>
<li class="chapter" data-level="12.2.2" data-path="supplementary-figure-07.html"><a href="supplementary-figure-07.html#computing-99.90-fst-percentiles"><i class="fa fa-check"></i><b>12.2.2</b> Computing 99.90 <em>F<sub>ST</sub></em> percentiles</a></li>
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<li class="chapter" data-level="13" data-path="supplementary-figure-08.html"><a href="supplementary-figure-08.html"><i class="fa fa-check"></i><b>13</b> Supplementary Figure 08</a><ul>
<li class="chapter" data-level="13.1" data-path="supplementary-figure-08.html"><a href="supplementary-figure-08.html#summary-9"><i class="fa fa-check"></i><b>13.1</b> Summary</a></li>
<li class="chapter" data-level="13.2" data-path="supplementary-figure-08.html"><a href="supplementary-figure-08.html#details-of-s08.r"><i class="fa fa-check"></i><b>13.2</b> Details of <code>S08.R</code></a></li>
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<li class="chapter" data-level="14" data-path="supplementary-figure-09.html"><a href="supplementary-figure-09.html"><i class="fa fa-check"></i><b>14</b> Supplementary Figure 09</a><ul>
<li class="chapter" data-level="14.1" data-path="supplementary-figure-09.html"><a href="supplementary-figure-09.html#summary-10"><i class="fa fa-check"></i><b>14.1</b> Summary</a></li>
<li class="chapter" data-level="14.2" data-path="supplementary-figure-09.html"><a href="supplementary-figure-09.html#details-of-s09.r"><i class="fa fa-check"></i><b>14.2</b> Details of <code>S09.R</code></a></li>
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<li class="chapter" data-level="15" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html"><i class="fa fa-check"></i><b>15</b> Supplementary Figure 10</a><ul>
<li class="chapter" data-level="15.1" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#summary-11"><i class="fa fa-check"></i><b>15.1</b> Summary</a></li>
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<li class="chapter" data-level="15.2" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#details-of-s10.r"><i class="fa fa-check"></i><b>15.2</b> Details of <code>S10.R</code></a><ul>
<li class="chapter" data-level="15.2.1" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#reading-in-data-2"><i class="fa fa-check"></i><b>15.2.1</b> Reading in Data</a></li>
<li class="chapter" data-level="15.2.2" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#subfigure-s10-a"><i class="fa fa-check"></i><b>15.2.2</b> Subfigure S10 a</a></li>
<li class="chapter" data-level="15.2.3" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#subfigure-s10-b"><i class="fa fa-check"></i><b>15.2.3</b> Subfigure S10 b</a></li>
<li class="chapter" data-level="15.2.4" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#subfigure-s10-c"><i class="fa fa-check"></i><b>15.2.4</b> Subfigure S10 c</a></li>
<li class="chapter" data-level="15.2.5" data-path="supplementary-figure-10.html"><a href="supplementary-figure-10.html#subfigure-s10-d"><i class="fa fa-check"></i><b>15.2.5</b> Subfigure S10 d</a></li>
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<li class="chapter" data-level="16" data-path="supplementary-figure-11.html"><a href="supplementary-figure-11.html"><i class="fa fa-check"></i><b>16</b> Supplementary Figure 11</a><ul>
<li class="chapter" data-level="16.1" data-path="supplementary-figure-11.html"><a href="supplementary-figure-11.html#summary-12"><i class="fa fa-check"></i><b>16.1</b> Summary</a></li>
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<li class="chapter" data-level="16.2" data-path="supplementary-figure-11.html"><a href="supplementary-figure-11.html#details-of-s11.r"><i class="fa fa-check"></i><b>16.2</b> Details of <code>S11.R</code></a></li>
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<li class="chapter" data-level="17" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html"><i class="fa fa-check"></i><b>17</b> Supplementary Figure 12</a><ul>
<li class="chapter" data-level="17.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-13"><i class="fa fa-check"></i><b>17.1</b> Summary</a></li>
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<li class="chapter" data-level="17.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>17.2</b> Details of <code>S12.R</code></a></li>
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<li class="chapter" data-level="18" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>18</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="18.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S13.R</code></a></li>
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<li class="chapter" data-level="19" data-path="supplementary-figure-14.html"><a href="supplementary-figure-14.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 14</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-14.html"><a href="supplementary-figure-14.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-14.html"><a href="supplementary-figure-14.html#details-of-s14.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S14.R</code></a></li>
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<li class="chapter" data-level="20" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html"><i class="fa fa-check"></i><b>20</b> Supplementary Figure 15</a><ul>
<li class="chapter" data-level="20.1" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html#summary-16"><i class="fa fa-check"></i><b>20.1</b> Summary</a></li>
<li class="chapter" data-level="20.2" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html#details-of-s15.r"><i class="fa fa-check"></i><b>20.2</b> Details of <code>S15.R</code></a><ul>
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<li class="chapter" data-level="20.2.1" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html#setup"><i class="fa fa-check"></i><b>20.2.1</b> Setup</a></li>
<li class="chapter" data-level="20.2.2" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html#subplots"><i class="fa fa-check"></i><b>20.2.2</b> Subplots</a></li>
<li class="chapter" data-level="20.2.3" data-path="supplementary-figure-15.html"><a href="supplementary-figure-15.html#composition"><i class="fa fa-check"></i><b>20.2.3</b> Composition</a></li>
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<li class="chapter" data-level="21" data-path="supplementary-figure-16.html"><a href="supplementary-figure-16.html"><i class="fa fa-check"></i><b>21</b> Supplementary Figure 16</a><ul>
<li class="chapter" data-level="21.1" data-path="supplementary-figure-16.html"><a href="supplementary-figure-16.html#summary-17"><i class="fa fa-check"></i><b>21.1</b> Summary</a></li>
<li class="chapter" data-level="21.2" data-path="supplementary-figure-16.html"><a href="supplementary-figure-16.html#details-of-s16.r"><i class="fa fa-check"></i><b>21.2</b> Details of <code>S16.R</code></a><ul>
<li class="chapter" data-level="21.2.1" data-path="supplementary-figure-16.html"><a href="supplementary-figure-16.html#setup-1"><i class="fa fa-check"></i><b>21.2.1</b> Setup</a></li>
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<li class="chapter" data-level="22" data-path="supplementary-figure-17.html"><a href="supplementary-figure-17.html"><i class="fa fa-check"></i><b>22</b> Supplementary Figure 17</a><ul>
<li class="chapter" data-level="22.1" data-path="supplementary-figure-17.html"><a href="supplementary-figure-17.html#summary-18"><i class="fa fa-check"></i><b>22.1</b> Summary</a></li>
<li class="chapter" data-level="22.2" data-path="supplementary-figure-17.html"><a href="supplementary-figure-17.html#details-of-s17.r"><i class="fa fa-check"></i><b>22.2</b> Details of <code>S17.R</code></a><ul>
<li class="chapter" data-level="22.2.1" data-path="supplementary-figure-17.html"><a href="supplementary-figure-17.html#additions-in-s17.plot_fun.r"><i class="fa fa-check"></i><b>22.2.1</b> Additions in <code>S17.plot_fun.R</code></a></li>
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<p>In the following, I give an overview over the individual steps done in during <em>de novo</em> assembly of the barred hamlet (<em>Hypoplectrus puella</em>) genome.</p>
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<p>Within the scheme, each arrow represents a script (or class of scripts) connecting individual steps of the assembly/ analysis.</p>
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