From 5e4509866b320571b6e8777d410824bdf71454ac Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 9 Jul 2024 00:21:26 +0000
Subject: [PATCH] site deploy

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Source  : 2fea52463b280fbf999ab433952e1e922677292b
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-06-07 13:42:11 +0000
Message : markdown source builds

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Source  : 564ffcd7aa54ea908ecc35bdfced36cbb067f464
Branch  : main
Author  : JCSzamosi <4465403+JCSzamosi@users.noreply.github.com>
Time    : 2024-06-07 13:41:27 +0000
Message : Merge pull request #164 from asntech/patch-1

Link to setup.html throws 404: fixes link to setup instructions.
---
 01-tidiness.html                    | 60 +++++++++++-----------
 02-project-planning.html            | 60 +++++++++++-----------
 03-ncbi-sra.html                    | 54 +++++++++----------
 404.html                            | 32 ++++++------
 CODE_OF_CONDUCT.html                | 34 ++++++------
 LICENSE.html                        | 46 ++++++++---------
 aio.html                            | 80 +++++++++++++++++------------
 data.html                           | 34 ++++++------
 discuss.html                        | 34 ++++++------
 images.html                         | 28 +++++-----
 index.html                          | 28 +++++-----
 instructor-notes.html               | 46 +++++++++--------
 instructor/01-tidiness.html         | 62 +++++++++++-----------
 instructor/02-project-planning.html | 62 +++++++++++-----------
 instructor/03-ncbi-sra.html         | 56 ++++++++++----------
 instructor/404.html                 | 32 ++++++------
 instructor/CODE_OF_CONDUCT.html     | 38 +++++++-------
 instructor/LICENSE.html             | 50 +++++++++---------
 instructor/aio.html                 | 80 +++++++++++++++++------------
 instructor/data.html                | 38 +++++++-------
 instructor/discuss.html             | 38 +++++++-------
 instructor/images.html              | 28 +++++-----
 instructor/index.html               | 28 +++++-----
 instructor/instructor-notes.html    | 46 +++++++++--------
 instructor/key-points.html          | 28 +++++-----
 instructor/old-ncbi.html            | 42 +++++++--------
 instructor/profiles.html            | 28 +++++-----
 instructor/reference.html           | 42 +++++++--------
 key-points.html                     | 28 +++++-----
 old-ncbi.html                       | 38 +++++++-------
 pkgdown.yml                         |  5 +-
 profiles.html                       | 28 +++++-----
 reference.html                      | 38 +++++++-------
 33 files changed, 703 insertions(+), 668 deletions(-)

diff --git a/01-tidiness.html b/01-tidiness.html
index 9d12b666..3755b31c 100644
--- a/01-tidiness.html
+++ b/01-tidiness.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -203,7 +203,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
-        
+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#introduction">Introduction</a></li>
@@ -212,7 +212,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#structuring-data-in-spreadsheets">Structuring data in spreadsheets</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -286,18 +286,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Home
         </a>
         <a class="chapter-link float-end" href="02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Tidiness</h1>
         <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -330,8 +330,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-</h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>When we think about the data for a sequencing project, we often start
 by thinking about the sequencing data that we get back from the
 sequencing center. However, equally or more important is the data you’ve
@@ -358,7 +358,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Types of files and information you have generated:</p>
 <ul><li>Spreadsheet or tabular data with the data from your experiment and
@@ -379,8 +379,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
 metadata, i.e. data about the data. We want to follow a few guidelines
 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
-</h2>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a></h2>
 <hr class="half-width"><p>Notes about your experiment, including how you prepared your samples
 for sequencing, should be in your lab notebook, whether that’s a
 physical lab notebook or electronic lab notebook. For guidelines on good
@@ -409,8 +409,8 @@ <h3 class="callout-title">Unique identifiers<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
-</h2>
+</section><section><h2 class="section-heading" id="data-about-the-experiment">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a></h2>
 <hr class="half-width"><p>Data about the experiment is usually collected in spreadsheets, like
 Excel.</p>
 <p>What type of data to collect depends on your experiment and there are
@@ -435,8 +435,8 @@ <h3 class="callout-title">Metadata standards<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
-</h2>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a></h2>
 <hr class="half-width"><p>Regardless of the type of data you’re collecting, there are standard
 ways to enter that data into the spreadsheet to make it easier to
 analyze later. We often enter data in a way that makes it easy for us as
@@ -487,7 +487,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -547,7 +547,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Home
         </a>
         <a class="chapter-link float-end" href="02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -558,18 +558,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -594,7 +594,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/01-tidiness.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-06-14",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/02-project-planning.html b/02-project-planning.html
index fd4d1a59..99c66e20 100644
--- a/02-project-planning.html
+++ b/02-project-planning.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -212,7 +212,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
-        
+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#sending-samples-to-the-facility">Sending samples to the facility</a></li>
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#summary">Summary</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -286,18 +286,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Planning for NGS Projects</h1>
         <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -358,8 +358,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
-</h2>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a></h2>
 <hr class="half-width"><p>The first step in sending your sample for sequencing will be to
 complete a form documenting the metadata for the facility. Take a look
 at the following example submission spreadsheet.</p>
@@ -388,7 +388,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul><li>Sequential order of well_position changes</li>
@@ -416,8 +416,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
-</h2>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a></h2>
 <hr class="half-width"><p>When the data come back from the sequencing facility, you will
 receive some documentation (metadata) as well as the sequence files
 themselves. Download and examine the following example file - here
@@ -450,7 +450,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Samples are organized by sample_id</li>
 <li>To relate filenames use the sample_id, and do a VLOOKUP on
@@ -469,8 +469,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a></h2>
 <hr class="half-width"><p>The raw data you get back from the sequencing center is the
 foundation of your sequencing analysis. You need to keep this data, so
 that you can always come back to it if there are any questions or you
@@ -505,8 +505,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Before analysis of data has begun, there are already many potential
 areas for errors and omissions. Keeping organized and keeping a critical
 eye can help catch mistakes.</p>
@@ -561,7 +561,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -572,18 +572,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -608,7 +608,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/02-project-planning.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/03-ncbi-sra.html b/03-ncbi-sra.html
index 7fe2551d..b7a301f5 100644
--- a/03-ncbi-sra.html
+++ b/03-ncbi-sra.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
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   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
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@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
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     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#accessing-the-original-archived-data">Accessing the original archived data</a></li>
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
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               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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             </div>
           </div><!-- /div.accordion -->
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@@ -293,11 +293,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Examining Data on the NCBI SRA Database</h1>
         <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
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+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -345,8 +345,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
-</h2>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a></h2>
 <hr class="half-width"><p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
 dataset (from Tenaillon, <em>et al.</em> 2016) adapted for this
 lesson</a> was obtained from the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI Sequence Read Archive</a>,
@@ -470,7 +470,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Escherichia coli B str. REL606 shown under the “organism” column.
 This is a tricky question because the column labeled “strain” actually
@@ -496,8 +496,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
-</h2>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a></h2>
 <hr class="half-width"><p>The SRA does not support direct download of fastq files from its
 webpage. However, the <a href="https://www.ebi.ac.uk/ena/browser/home" class="external-link">European Nucleotide
 Archive</a> does. Let’s see how we can get a download link to a file we
@@ -515,8 +515,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
-</h2>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class="anchor" aria-label="anchor" href="#about-the-sequence-read-archive"></a></h3>
 <ul><li>You can learn more about the SRA by reading the <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/" class="external-link">SRA
@@ -526,8 +526,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 Toolkit</a>
 </li>
 </ul></div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -571,18 +571,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
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+
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-        
+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -607,7 +607,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/03-ncbi-sra.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-11-20",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 9306d9dc..01bbd0ec 100644
--- a/404.html
+++ b/404.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
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                 </div><!--/div.accordion-flush-->
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           <div class="accordion accordion-flush" id="accordionFlush11">
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         <a href="https://datacarpentry.github.io/organization-genomics/index.html" class="external-link">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -202,7 +202,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/01-tidiness.html" class="external-link">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
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         <a href="https://datacarpentry.github.io/organization-genomics/02-project-planning.html" class="external-link">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/03-ncbi-sra.html" class="external-link">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -258,10 +258,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="https://datacarpentry.github.io/organization-genomics/aio.html" class="external-link">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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         <h1>Page not found</h1>
         
-<section id="our-apologies"><h2 class="section-heading">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-</h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
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@@ -297,18 +297,18 @@ <h1>Page not found</h1>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -332,8 +332,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/organization-genomics/404.html",
   "identifier": "https://datacarpentry.github.io/organization-genomics/404.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 2bdc5093..587d3d65 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -46,7 +46,7 @@
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           </ul></li>
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       <div class="dropdown" id="instructor-dropdown">
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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@@ -279,11 +279,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
         <p>Last updated on 2023-05-02 |
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@@ -322,18 +322,18 @@ <h1>Contributor Code of Conduct</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
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+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -358,7 +358,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 59c1aeaf..d591e458 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
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             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,19 +279,19 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
 
-<section id="instructional-material"><h2 class="section-heading">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-</h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
+<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
 Carpentry) instructional material is made available under the <a href="https://creativecommons.org/licenses/by/4.0/" class="external-link">Creative Commons
 Attribution license</a>. The following is a human-readable summary of
@@ -324,8 +324,8 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section id="software"><h2 class="section-heading">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
+<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -345,8 +345,8 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
-</section><section id="trademark"><h2 class="section-heading">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
-</h2>
+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
+<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -373,18 +373,18 @@ <h1>Licenses</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -409,7 +409,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/LICENSE.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index eba96bc6..1fda361c 100644
--- a/aio.html
+++ b/aio.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -204,7 +204,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
 </div>
 <!--/div.mobile-row -->
@@ -226,7 +226,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -238,7 +238,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -250,7 +250,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -262,7 +262,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -301,11 +301,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -326,7 +326,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <section id="aio-01-tidiness"><p>Content from <a href="01-tidiness.html">Data Tidiness</a></p>
 <hr>
 <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -361,7 +361,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>When we think about the data for a sequencing project, we often start
@@ -390,7 +391,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Types of files and information you have generated:</p>
 <ul>
@@ -413,7 +414,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <p>All of the data and information just discussed can be considered
 metadata, i.e. data about the data. We want to follow a few guidelines
 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a>
 </h2>
 <hr class="half-width">
 <p>Notes about your experiment, including how you prepared your samples
@@ -444,7 +446,8 @@ <h3 class="callout-title">Unique identifiers<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+</section><section><h2 class="section-heading" id="data-about-the-experiment">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
+<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
 </h2>
 <hr class="half-width">
 <p>Data about the experiment is usually collected in spreadsheets, like
@@ -471,7 +474,8 @@ <h3 class="callout-title">Metadata standards<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section id="structuring-data-in-spreadsheets"><h2 class="section-heading">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
 </h2>
 <hr class="half-width">
 <p>Regardless of the type of data you’re collecting, there are standard
@@ -526,7 +530,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -580,7 +584,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-project-planning"><p>Content from <a href="02-project-planning.html">Planning for NGS Projects</a></p>
 <hr>
 <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -643,7 +647,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>The first step in sending your sample for sequencing will be to
@@ -676,7 +681,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul>
@@ -712,7 +717,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>When the data come back from the sequencing facility, you will
@@ -751,7 +757,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Samples are organized by sample_id</li>
@@ -772,7 +778,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a>
 </h2>
 <hr class="half-width">
 <p>The raw data you get back from the sequencing center is the
@@ -813,7 +820,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Before analysis of data has begun, there are already many potential
@@ -863,7 +871,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-ncbi-sra"><p>Content from <a href="03-ncbi-sra.html">Examining Data on the NCBI SRA Database</a></p>
 <hr>
 <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -913,7 +921,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
@@ -1048,7 +1057,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Escherichia coli B str. REL606 shown under the “organism” column.
@@ -1076,7 +1085,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
 </h2>
 <hr class="half-width">
 <p>The SRA does not support direct download of fastq files from its
@@ -1098,7 +1108,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -1113,7 +1124,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 </li>
 </ul>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -1150,18 +1162,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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+
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         <a href="index.html">Summary and Setup</a>
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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               </div>
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             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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         <h1>Data</h1>
         <p>Last updated on 2023-05-02 |
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
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         <a href="index.html">Summary and Setup</a>
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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+
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@@ -315,18 +315,18 @@ <h1>Discussion</h1>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/discuss.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 <div class="d-grid gap-1">
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 <!-- /div.accordion -->
@@ -369,18 +369,18 @@ <h3 id="03-ncbi-sra-figure-5">Figure 5</h3>
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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   </script><script>
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             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/index.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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diff --git a/instructor-notes.html b/instructor-notes.html
index 9eebf1ec..da238be4 100644
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+++ b/instructor-notes.html
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@@ -204,7 +204,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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 <!--/div.accordion-header-->
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+
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         <a href="01-tidiness.html">1. Data Tidiness</a>
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 <!--/div.accordion-header-->
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+
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+<section><h2 class="section-heading" id="instructor-notes">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
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-</section><section id="lesson-design"><h2 class="section-heading">Lesson design<a class="anchor" aria-label="anchor" href="#lesson-design"></a>
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+</section><section><h2 class="section-heading" id="working-with-participants-level-of-expertise">Working with participants’ level of expertise<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-participants-level-of-expertise"></a>
 </h2>
 <hr class="half-width">
 <p>Learners may be taking this lesson for many reasons - they may be
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 </div>
-</section><section id="technical-tips-and-tricks"><h2 class="section-heading">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
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+<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
 </h2>
 <hr class="half-width">
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 suit the learning environment.</p>
-</section><section id="common-problems"><h2 class="section-heading">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+</section><section><h2 class="section-heading" id="common-problems">Common problems<a class="anchor" aria-label="anchor" href="#common-problems"></a>
+<a class="anchor" aria-label="anchor" href="#common-problems"></a>
 </h2>
 <hr class="half-width">
 <div class="section level4">
@@ -492,18 +498,18 @@ <h4 id="people-are-not-interactive-or-responsive-on-the-exercises">People are no
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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-  "dateModified": "2024-07-02",
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diff --git a/instructor/01-tidiness.html b/instructor/01-tidiness.html
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+
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+
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
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               </div>
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
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+
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           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Tidiness</h1>
         <p>Last updated on 2023-06-14 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
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 </div>
 </div>
 </div>
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-</h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>When we think about the data for a sequencing project, we often start
 by thinking about the sequencing data that we get back from the
 sequencing center. However, equally or more important is the data you’ve
@@ -360,7 +360,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 <p>Types of files and information you have generated:</p>
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 for metadata.</p>
-</section><section id="notes"><h2 class="section-heading">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
-</h2>
+</section><section><h2 class="section-heading" id="notes">Notes<a class="anchor" aria-label="anchor" href="#notes"></a>
+<a class="anchor" aria-label="anchor" href="#notes"></a></h2>
 <hr class="half-width"><p>Notes about your experiment, including how you prepared your samples
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-</section><section id="data-about-the-experiment"><h2 class="section-heading">Data about the experiment<a class="anchor" aria-label="anchor" href="#data-about-the-experiment"></a>
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 <hr class="half-width"><p>Data about the experiment is usually collected in spreadsheets, like
 Excel.</p>
 <p>What type of data to collect depends on your experiment and there are
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 </div>
 </div>
 </div>
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-</h2>
+</section><section><h2 class="section-heading" id="structuring-data-in-spreadsheets">Structuring data in spreadsheets<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a>
+<a class="anchor" aria-label="anchor" href="#structuring-data-in-spreadsheets"></a></h2>
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 ways to enter that data into the spreadsheet to make it easier to
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 <div class="accordion-body">
 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -549,7 +549,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-project-planning.html" rel="next">
-          Next: Planning for NGS... 
+          Next: Planning for NGS...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/01-tidiness.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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diff --git a/instructor/02-project-planning.html b/instructor/02-project-planning.html
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+++ b/instructor/02-project-planning.html
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+
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         <a href="index.html">Summary and Schedule</a>
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+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#sending-samples-to-the-facility">Sending samples to the facility</a></li>
@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#summary">Summary</a></li>
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@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
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@@ -286,20 +286,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="../instructor/03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Planning for NGS Projects</h1>
         <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -360,8 +360,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
-</h2>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a></h2>
 <hr class="half-width"><p>The first step in sending your sample for sequencing will be to
 complete a form documenting the metadata for the facility. Take a look
 at the following example submission spreadsheet.</p>
@@ -390,7 +390,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Errors:</p>
 <ul><li>Sequential order of well_position changes</li>
@@ -418,8 +418,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
-</h2>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a></h2>
 <hr class="half-width"><p>When the data come back from the sequencing facility, you will
 receive some documentation (metadata) as well as the sequence files
 themselves. Download and examine the following example file - here
@@ -452,7 +452,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Samples are organized by sample_id</li>
 <li>To relate filenames use the sample_id, and do a VLOOKUP on
@@ -471,8 +471,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="storing-data">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
+<a class="anchor" aria-label="anchor" href="#storing-data"></a></h2>
 <hr class="half-width"><p>The raw data you get back from the sequencing center is the
 foundation of your sequencing analysis. You need to keep this data, so
 that you can always come back to it if there are any questions or you
@@ -507,8 +507,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Before analysis of data has begun, there are already many potential
 areas for errors and omissions. Keeping organized and keeping a critical
 eye can help catch mistakes.</p>
@@ -563,7 +563,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Tidiness
         </a>
         <a class="chapter-link float-end" href="../instructor/03-ncbi-sra.html" rel="next">
-          Next: Examining Data on... 
+          Next: Examining Data on...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -574,18 +574,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -610,7 +610,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/02-project-planning.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/03-ncbi-sra.html b/instructor/03-ncbi-sra.html
index 540e581c..d5033e43 100644
--- a/instructor/03-ncbi-sra.html
+++ b/instructor/03-ncbi-sra.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
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@@ -221,7 +221,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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       <div class="accordion-body">
         <ul><li><a href="#accessing-the-original-archived-data">Accessing the original archived data</a></li>
@@ -230,7 +230,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
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@@ -262,10 +262,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -293,13 +293,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Examining Data on the NCBI SRA Database</h1>
         <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -347,8 +347,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
-</h2>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a></h2>
 <hr class="half-width"><p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
 dataset (from Tenaillon, <em>et al.</em> 2016) adapted for this
 lesson</a> was obtained from the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI Sequence Read Archive</a>,
@@ -472,7 +472,7 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Escherichia coli B str. REL606 shown under the “organism” column.
 This is a tricky question because the column labeled “strain” actually
@@ -498,8 +498,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
-</h2>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a></h2>
 <hr class="half-width"><p>The SRA does not support direct download of fastq files from its
 webpage. However, the <a href="https://www.ebi.ac.uk/ena/browser/home" class="external-link">European Nucleotide
 Archive</a> does. Let’s see how we can get a download link to a file we
@@ -517,8 +517,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
-</h2>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class="anchor" aria-label="anchor" href="#about-the-sequence-read-archive"></a></h3>
 <ul><li>You can learn more about the SRA by reading the <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/" class="external-link">SRA
@@ -528,8 +528,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 Toolkit</a>
 </li>
 </ul></div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -573,18 +573,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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-        
+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -609,7 +609,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/03-ncbi-sra.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-11-20",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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--- a/instructor/404.html
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           </ul></li>
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
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@@ -191,7 +191,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/index.html" class="external-link">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -202,7 +202,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/01-tidiness.html" class="external-link">1. Data Tidiness</a>
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 <!--/div.accordion-header-->
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         <a href="https://datacarpentry.github.io/organization-genomics/02-project-planning.html" class="external-link">2. Planning for NGS Projects</a>
     </div>
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="https://datacarpentry.github.io/organization-genomics/03-ncbi-sra.html" class="external-link">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
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@@ -258,10 +258,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
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             <hr class="half-width resources"><a href="https://datacarpentry.github.io/organization-genomics/instructor/aio.html" class="external-link">See all in one page</a>
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+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
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@@ -297,18 +297,18 @@ <h1>Page not found</h1>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
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@@ -46,7 +46,7 @@
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+
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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         <h1>Contributor Code of Conduct</h1>
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+
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       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
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           </div><!-- /div.accordion -->
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@@ -279,21 +279,21 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
-        
-        
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+
+
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         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
 
-<section id="instructional-material"><h2 class="section-heading">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
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+<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
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 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section id="software"><h2 class="section-heading">Software<a class="anchor" aria-label="anchor" href="#software"></a>
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+<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -347,8 +347,8 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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-</section><section id="trademark"><h2 class="section-heading">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
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 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -375,18 +375,18 @@ <h1>Licenses</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/LICENSE.md" class="external-link">Edit on GitHub</a>
-        
+
 	
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
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     </div>
 <!--/div.accordion-header-->
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+
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             <hr class="half-width resources">
 <a href="../instructor/aio.html">See all in one page</a>
-            
+
 
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 <div class="d-grid gap-1">
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-        
+
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 </div>
 </div>
 </div>
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 </h2>
 <hr class="half-width">
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 <ul>
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 </h2>
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+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <p>A full set of types of issues with spreadsheet data is at the <a href="https://www.datacarpentry.org/spreadsheet-ecology-lesson/02-common-mistakes/" class="external-link">Data
 Carpentry Ecology spreadsheet lesson</a>. Not all are present in this
@@ -587,7 +591,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-project-planning"><p>Content from <a href="02-project-planning.html">Planning for NGS Projects</a></p>
 <hr>
 <p>Last updated on 2024-04-04 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/02-project-planning.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
 <div class="text-end">
@@ -651,7 +655,8 @@ <h3 class="callout-title">Discussion<a class="anchor" aria-label="anchor" href="
 </div>
 </div>
 </div>
-<section id="sending-samples-to-the-facility"><h2 class="section-heading">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<section><h2 class="section-heading" id="sending-samples-to-the-facility">Sending samples to the facility<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#sending-samples-to-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>The first step in sending your sample for sequencing will be to
@@ -684,7 +689,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="accordion-body">
 <p>Errors:</p>
 <ul>
@@ -720,7 +725,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="retrieving-sample-sequencing-data-from-the-facility"><h2 class="section-heading">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+</section><section><h2 class="section-heading" id="retrieving-sample-sequencing-data-from-the-facility">Retrieving sample sequencing data from the facility<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
+<a class="anchor" aria-label="anchor" href="#retrieving-sample-sequencing-data-from-the-facility"></a>
 </h2>
 <hr class="half-width">
 <p>When the data come back from the sequencing facility, you will
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 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Samples are organized by sample_id</li>
@@ -780,7 +786,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="storing-data"><h2 class="section-heading">Storing data<a class="anchor" aria-label="anchor" href="#storing-data"></a>
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+<a class="anchor" aria-label="anchor" href="#storing-data"></a>
 </h2>
 <hr class="half-width">
 <p>The raw data you get back from the sequencing center is the
@@ -821,7 +828,8 @@ <h4 id="some-data-storage-solutions">Some data storage solutions<a class="anchor
 to Cloud Computing for Genomics”</a>.</p>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Before analysis of data has begun, there are already many potential
@@ -871,7 +879,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-ncbi-sra"><p>Content from <a href="03-ncbi-sra.html">Examining Data on the NCBI SRA Database</a></p>
 <hr>
 <p>Last updated on 2023-11-20 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/episodes/03-ncbi-sra.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
 <div class="text-end">
@@ -922,7 +930,8 @@ <h3 class="card-title">Objectives</h3>
 (SRA)</a> is the database we will be using for this lesson, but the
 EMBL-EBI’s Nucleotide Archive (ENA) is also useful. The general
 processes are similar for any database.</p>
-<section id="accessing-the-original-archived-data"><h2 class="section-heading">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<section><h2 class="section-heading" id="accessing-the-original-archived-data">Accessing the original archived data<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
+<a class="anchor" aria-label="anchor" href="#accessing-the-original-archived-data"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="https://www.datacarpentry.org/organization-genomics/data" class="external-link">sequencing
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Escherichia coli B str. REL606 shown under the “organism” column.
@@ -1085,7 +1094,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 changes. If you were to save this file, make sure you save it as a
 text-based <code>.csv</code> file format.</p>
 </div>
-</section><section id="downloading-a-few-sequencing-files-embl-ebi"><h2 class="section-heading">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+</section><section><h2 class="section-heading" id="downloading-a-few-sequencing-files-embl-ebi">Downloading a few sequencing files: EMBL-EBI<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
+<a class="anchor" aria-label="anchor" href="#downloading-a-few-sequencing-files-embl-ebi"></a>
 </h2>
 <hr class="half-width">
 <p>The SRA does not support direct download of fastq files from its
@@ -1107,7 +1117,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 this way. For that, the NCBI has made a software package called the
 <code>sra-toolkit</code>. However, for a couple files, it’s often easier
 to go through the ENA.</p>
-</section><section id="where-to-learn-more"><h2 class="section-heading">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="where-to-learn-more">Where to learn more<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -1122,7 +1133,8 @@ <h3 id="about-the-sequence-read-archive">About the Sequence Read Archive<a class
 </li>
 </ul>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -1159,18 +1171,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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-  "dateModified": "2024-07-02",
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diff --git a/instructor/data.html b/instructor/data.html
index 0f1e0e29..b20564a2 100644
--- a/instructor/data.html
+++ b/instructor/data.html
@@ -46,7 +46,7 @@
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               </div><!--div.sidenav-view-selector -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
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     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
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   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -279,13 +279,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -404,18 +404,18 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/data.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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   "dateCreated": "2015-03-24",
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diff --git a/instructor/discuss.html b/instructor/discuss.html
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@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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           <div class="accordion accordion-flush" id="accordionFlush11">
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     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -279,13 +279,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
         <p>Last updated on 2023-05-02 |
-        
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         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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         </div>
@@ -317,18 +317,18 @@ <h1>Discussion</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/discuss.md" class="external-link">Edit on GitHub</a>
-        
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         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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-        
+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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+
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@@ -375,18 +375,18 @@ <h3 id="03-ncbi-sra-figure-5">Figure 5</h3>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
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+
 	
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 			</div>
 			<div class="col-md-6">
-        
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-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/index.md" class="external-link">Edit on GitHub</a>
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+
 	
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 			</div>
 			<div class="col-md-6">
-        
+
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+
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
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 <!--/div.accordion-header-->
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-<section id="instructor-notes"><h2 class="section-heading">Instructor notes<a class="anchor" aria-label="anchor" href="#instructor-notes"></a>
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 <hr class="half-width">
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 </div>
-</section><section id="technical-tips-and-tricks"><h2 class="section-heading">Technical tips and tricks<a class="anchor" aria-label="anchor" href="#technical-tips-and-tricks"></a>
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 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+
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 <!--/div.accordion-header-->
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             <hr class="half-width resources">
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-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
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@@ -360,18 +360,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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-        
+
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@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
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@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
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 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,20 +279,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Old NCBI</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
-        
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+
+
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+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="original-older-ncbi-instructions"><h2 class="section-heading">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
-</h2>
+<section><h2 class="section-heading" id="original-older-ncbi-instructions">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
+<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a></h2>
 <hr class="half-width"><p>These will be phased out of our lesson when NCBI stops supporting the
 old page versions.</p>
 <ol style="list-style-type: decimal"><li><p>Access the Tenaillon dataset from the provided link: <a href="https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605" class="external-link">https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605</a>.
@@ -339,18 +339,18 @@ <h1>Old NCBI</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -375,7 +375,7 @@ <h1>Old NCBI</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/old-ncbi.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index aeadbe2d..97b59f8a 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
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       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
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             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -274,18 +274,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -309,8 +309,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/organization-genomics/instructor/profiles.html",
   "identifier": "https://datacarpentry.github.io/organization-genomics/instructor/profiles.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 780a28cd..0e9731b5 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -46,7 +46,7 @@
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           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
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             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,20 +279,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Glossary</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
-</h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
+<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
 <hr class="half-width"><p>{:auto_ids}<br>
 accession : a unique identifier assigned to each sequence or set of
 sequences</p>
@@ -415,18 +415,18 @@ <h1>Glossary</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -451,7 +451,7 @@ <h1>Glossary</h1>
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   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
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+  "datePublished": "2024-07-09"
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diff --git a/key-points.html b/key-points.html
index 1cc28856..0a1ee03a 100644
--- a/key-points.html
+++ b/key-points.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
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       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -204,7 +204,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
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             <hr>
 </div>
 <!--/div.mobile-row -->
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         <a href="index.html">Summary and Setup</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -238,7 +238,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
@@ -250,7 +250,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div>
 <!--/div.accordion-header-->
-        
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 <!--/div.accordion-item-->
 </div>
@@ -262,7 +262,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div>
 <!--/div.accordion-header-->
-        
+
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 <!--/div.accordion-item-->
 </div>
@@ -301,11 +301,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
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           </div>
 <!-- /div.accordion -->
@@ -354,18 +354,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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 			</div>
@@ -390,8 +390,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://datacarpentry.github.io/organization-genomics/key-points.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/old-ncbi.html b/old-ncbi.html
index 1ede1504..d1116019 100644
--- a/old-ncbi.html
+++ b/old-ncbi.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
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 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
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 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
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             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,18 +279,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Old NCBI</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="original-older-ncbi-instructions"><h2 class="section-heading">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
-</h2>
+<section><h2 class="section-heading" id="original-older-ncbi-instructions">Original (older) NCBI instructions<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a>
+<a class="anchor" aria-label="anchor" href="#original-older-ncbi-instructions"></a></h2>
 <hr class="half-width"><p>These will be phased out of our lesson when NCBI stops supporting the
 old page versions.</p>
 <ol style="list-style-type: decimal"><li><p>Access the Tenaillon dataset from the provided link: <a href="https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605" class="external-link">https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP064605</a>.
@@ -337,18 +337,18 @@ <h1>Old NCBI</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/instructors/old-ncbi.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -373,7 +373,7 @@ <h1>Old NCBI</h1>
   "identifier": "https://datacarpentry.github.io/organization-genomics/old-ncbi.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 99d5f1ac..a63693d8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,5 @@
 pandoc: 3.1.11
-pkgdown: 2.0.9
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-02T00:22Z
-
+last_built: 2024-07-09T00:21Z
diff --git a/profiles.html b/profiles.html
index 60b212c8..75604507 100644
--- a/profiles.html
+++ b/profiles.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -274,18 +274,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -309,8 +309,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/organization-genomics/profiles.html",
   "identifier": "https://datacarpentry.github.io/organization-genomics/profiles.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index c77f5be6..b159b4d1 100644
--- a/reference.html
+++ b/reference.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -170,7 +170,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -189,7 +189,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -198,7 +198,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-tidiness.html">1. Data Tidiness</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -207,7 +207,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-project-planning.html">2. Planning for NGS Projects</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -216,7 +216,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-ncbi-sra.html">3. Examining Data on the NCBI SRA Database</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -248,10 +248,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -279,18 +279,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Glossary</h1>
         <p>Last updated on 2023-05-02 |
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
 
         
-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
-</h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
+<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
 <hr class="half-width"><p>{:auto_ids}<br>
 accession : a unique identifier assigned to each sequence or set of
 sequences</p>
@@ -413,18 +413,18 @@ <h1>Glossary</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/datacarpentry/organization-genomics/edit/main/learners/reference.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/datacarpentry/organization-genomics/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/datacarpentry/organization-genomics/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/datacarpentry/organization-genomics/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:team@carpentries.org">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -449,7 +449,7 @@ <h1>Glossary</h1>
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   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-02",
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+  "datePublished": "2024-07-09"
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