From 706c424201935fb61ef9b266f3320e665b342a4e Mon Sep 17 00:00:00 2001
From: lizgehret <lizgehret@users.noreply.github.com>
Date: Sat, 30 Mar 2024 13:06:12 +0000
Subject: [PATCH] deploy: 423d053ad76806d750a5c1c589fe742101863d37

---
 80-leiden-tutorial.html        | 40 ++++++++++++++++++++++++++++++++++
 _sources/80-leiden-tutorial.md | 17 +++++++++++++++
 searchindex.js                 |  2 +-
 3 files changed, 58 insertions(+), 1 deletion(-)

diff --git a/80-leiden-tutorial.html b/80-leiden-tutorial.html
index 5724059..32bf7ea 100644
--- a/80-leiden-tutorial.html
+++ b/80-leiden-tutorial.html
@@ -418,6 +418,11 @@ <h2> Contents </h2>
 </li>
 </ul>
 </li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#breakout-session">Breakout Session</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#group-a">Group A</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#group-b">Group B</a></li>
+</ul>
+</li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#mag-based-analysis">MAG-based analysis</a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#busco-qc">BUSCO QC</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#obtaining-our-kraken2-reports">Obtaining our Kraken2 reports</a></li>
@@ -881,6 +886,36 @@ <h4>Emperor Plot Creation for gene diversity<a class="headerlink" href="#emperor
 </section>
 </section>
 </section>
+<section id="breakout-session">
+<h2>Breakout Session<a class="headerlink" href="#breakout-session" title="Permalink to this heading">#</a></h2>
+<p>Before we begin the final segment of our analysis in this workshop, we’re going to break off into two groups for a small interactive exercise! We will assign you to either group A or B, and will go through your respective exercises below.</p>
+<section id="group-a">
+<h3>Group A<a class="headerlink" href="#group-a" title="Permalink to this heading">#</a></h3>
+<p>In this group exercise we will be examining the correlation between our Jaccard distance matrices for reads and contigs. We will not be providing commands for this, so do some poking around in the help text for commands within the diversity plugin to see what might make sense for comparing these two distance matrices. :)</p>
+<details class="sd-sphinx-override sd-dropdown sd-card sd-mb-3">
+<summary class="sd-summary-title sd-card-header">
+Hint!<div class="sd-summary-down docutils">
+<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-down" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M5.22 8.72a.75.75 0 000 1.06l6.25 6.25a.75.75 0 001.06 0l6.25-6.25a.75.75 0 00-1.06-1.06L12 14.44 6.28 8.72a.75.75 0 00-1.06 0z"></path></svg></div>
+<div class="sd-summary-up docutils">
+<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-up" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M18.78 15.28a.75.75 0 000-1.06l-6.25-6.25a.75.75 0 00-1.06 0l-6.25 6.25a.75.75 0 101.06 1.06L12 9.56l5.72 5.72a.75.75 0 001.06 0z"></path></svg></div>
+</summary><div class="sd-summary-content sd-card-body docutils">
+<p class="sd-card-text">Try running <code class="docutils literal notranslate"><span class="pre">qiime</span> <span class="pre">diversity</span> <span class="pre">--help</span></code> to view all of the available methods within this plugin. From here, you can run the <code class="docutils literal notranslate"><span class="pre">--help</span></code> command on any of the methods to learn more about their inputs and functionality (i.e. <code class="docutils literal notranslate"><span class="pre">qiime</span> <span class="pre">diversity</span> <span class="pre">beta</span> <span class="pre">--help</span></code>).</p>
+</div>
+</details></section>
+<section id="group-b">
+<h3>Group B<a class="headerlink" href="#group-b" title="Permalink to this heading">#</a></h3>
+<p>In this group exercise we will be examining the correlation between our read-based Jaccard distance matrix and a read-based Bray-Curtis distance matrix. Note that you’ll need to first generate the Bray-Curtis distance matrix before you can move forward with this comparison. We will not be providing commands for this, so do some poking around in the help text for commands within the diversity plugin to see what might make sense for comparing these two distance matrices. :)</p>
+<details class="sd-sphinx-override sd-dropdown sd-card sd-mb-3">
+<summary class="sd-summary-title sd-card-header">
+Hint!<div class="sd-summary-down docutils">
+<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-down" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M5.22 8.72a.75.75 0 000 1.06l6.25 6.25a.75.75 0 001.06 0l6.25-6.25a.75.75 0 00-1.06-1.06L12 14.44 6.28 8.72a.75.75 0 00-1.06 0z"></path></svg></div>
+<div class="sd-summary-up docutils">
+<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-up" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M18.78 15.28a.75.75 0 000-1.06l-6.25-6.25a.75.75 0 00-1.06 0l-6.25 6.25a.75.75 0 101.06 1.06L12 9.56l5.72 5.72a.75.75 0 001.06 0z"></path></svg></div>
+</summary><div class="sd-summary-content sd-card-body docutils">
+<p class="sd-card-text">Try running <code class="docutils literal notranslate"><span class="pre">qiime</span> <span class="pre">diversity</span> <span class="pre">--help</span></code> to view all of the available methods within this plugin. From here, you can run the <code class="docutils literal notranslate"><span class="pre">--help</span></code> command on any of the methods to learn more about their inputs and functionality (i.e. <code class="docutils literal notranslate"><span class="pre">qiime</span> <span class="pre">diversity</span> <span class="pre">beta</span> <span class="pre">--help</span></code>).</p>
+</div>
+</details></section>
+</section>
 <section id="mag-based-analysis">
 <h2>MAG-based analysis<a class="headerlink" href="#mag-based-analysis" title="Permalink to this heading">#</a></h2>
 <div class="toggle docutils container">
@@ -1131,6 +1166,11 @@ <h2>Provenance Replay<a class="headerlink" href="#provenance-replay" title="Perm
 </li>
 </ul>
 </li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#breakout-session">Breakout Session</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#group-a">Group A</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#group-b">Group B</a></li>
+</ul>
+</li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#mag-based-analysis">MAG-based analysis</a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#busco-qc">BUSCO QC</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#obtaining-our-kraken2-reports">Obtaining our Kraken2 reports</a></li>
diff --git a/_sources/80-leiden-tutorial.md b/_sources/80-leiden-tutorial.md
index ca44f06..19f9ef0 100644
--- a/_sources/80-leiden-tutorial.md
+++ b/_sources/80-leiden-tutorial.md
@@ -423,6 +423,23 @@ qiime emperor plot \
   --o-visualization ./contigs/jaccard-diamond-autofmt-pcoa-contigs.qzv
 ```
 
+## Breakout Session
+Before we begin the final segment of our analysis in this workshop, we're going to break off into two groups for a small interactive exercise! We will assign you to either group A or B, and will go through your respective exercises below.
+
+#### Group A
+In this group exercise we will be examining the correlation between our Jaccard distance matrices for reads and contigs. We will not be providing commands for this, so do some poking around in the help text for commands within the diversity plugin to see what might make sense for comparing these two distance matrices. :)
+
+````{dropdown} Hint!
+Try running `qiime diversity --help` to view all of the available methods within this plugin. From here, you can run the `--help` command on any of the methods to learn more about their inputs and functionality (i.e. `qiime diversity beta --help`).
+````
+
+#### Group B
+In this group exercise we will be examining the correlation between our read-based Jaccard distance matrix and a read-based Bray-Curtis distance matrix. Note that you'll need to first generate the Bray-Curtis distance matrix before you can move forward with this comparison. We will not be providing commands for this, so do some poking around in the help text for commands within the diversity plugin to see what might make sense for comparing these two distance matrices. :)
+
+````{dropdown} Hint!
+Try running `qiime diversity --help` to view all of the available methods within this plugin. From here, you can run the `--help` command on any of the methods to learn more about their inputs and functionality (i.e. `qiime diversity beta --help`).
+````
+
 ## MAG-based analysis
 ````{toggle}
 Let's start binning our contigs into MAGs using various tools and methodologies!
diff --git a/searchindex.js b/searchindex.js
index 4f6459b..889d1c5 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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