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index 0615596..e009aa8 100644
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+++ b/.quarto/crossref/index.qmd/index.html.json
@@ -1 +1 @@
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\ No newline at end of file
+{"headings":["preface"],"entries":[],"options":{"chapters":true}}
\ No newline at end of file
diff --git a/.quarto/crossref/references.qmd/references.html.json b/.quarto/crossref/references.qmd/references.html.json
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+++ b/.quarto/crossref/references.qmd/references.html.json
@@ -1 +1 @@
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+{"headings":[],"entries":[],"options":{"chapters":true}}
\ No newline at end of file
diff --git a/demo-genome-searching_cache/html/__packages b/demo-genome-searching_cache/html/__packages
index a86d057..7b64a0c 100644
--- a/demo-genome-searching_cache/html/__packages
+++ b/demo-genome-searching_cache/html/__packages
@@ -1,10 +1,3 @@
-base
-methods
-datasets
-utils
-grDevices
-graphics
-stats
 tidyverse
 ggplot2
 tibble
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new file mode 100644
index 0000000..b3f8c58
--- /dev/null
+++ b/demo-phylogenetics_cache/html/__packages
@@ -0,0 +1,5 @@
+ggplot2
+dplyr
+stringr
+ape
+ggtree
diff --git a/demo-phylogenetics_cache/html/unnamed-chunk-1_5f67f100fe84738a6334ee503853aa01.RData b/demo-phylogenetics_cache/html/unnamed-chunk-1_5f67f100fe84738a6334ee503853aa01.RData
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diff --git a/docs/demo-genome-assembly.html b/docs/demo-genome-assembly.html
index 298307e..03da44a 100644
--- a/docs/demo-genome-assembly.html
+++ b/docs/demo-genome-assembly.html
@@ -298,8 +298,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
     <h2 id="toc-title">Table of contents</h2>
    
   <ul>
-  <li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#download-the-reads" id="toc-download-the-reads" class="nav-link" data-scroll-target="#download-the-reads">Download the reads</a></li>
+  <li><a href="#download-the-reads" id="toc-download-the-reads" class="nav-link active" data-scroll-target="#download-the-reads">Download the reads</a></li>
   <li><a href="#assess-read-qualities" id="toc-assess-read-qualities" class="nav-link" data-scroll-target="#assess-read-qualities">Assess read qualities</a></li>
   <li><a href="#exploring-assemblers" id="toc-exploring-assemblers" class="nav-link" data-scroll-target="#exploring-assemblers">Exploring assemblers</a>
   <ul class="collapse">
@@ -334,11 +333,20 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">15</span>&nbsp;
 
 </header>
 
-<section id="challenge" class="level2 unnumbered">
-<h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+<div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs.&nbsp;sequence lengths (log transformed) and ii) the read length vs.&nbsp;read quality vs.&nbsp;read number.</p>
 <p>He ask you to document every step and to conclude what data should be used.</p>
-</section>
+</div>
+</div>
 <section id="download-the-reads" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="download-the-reads">Download the reads</h2>
 <div class="sourceCode" id="downloading-seqs"><pre class="sourceCode zsh important code-with-copy"><code class="sourceCode zsh"><span id="downloading-seqs-1"><a href="#downloading-seqs-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
diff --git a/docs/demo-genome-searching.html b/docs/demo-genome-searching.html
index b3b8115..41c7934 100644
--- a/docs/demo-genome-searching.html
+++ b/docs/demo-genome-searching.html
@@ -272,17 +272,12 @@ <h1 class="quarto-secondary-nav-title">
         <nav id="TOC" role="doc-toc"><h2 id="toc-title">Table of contents</h2>
    
   <ul>
-<li>
-<a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a>
-  <ul class="collapse">
-<li><a href="#downloading-a-genome" id="toc-downloading-a-genome" class="nav-link" data-scroll-target="#downloading-a-genome">Downloading a genome</a></li>
+<li><a href="#downloading-a-genome" id="toc-downloading-a-genome" class="nav-link active" data-scroll-target="#downloading-a-genome">Downloading a genome</a></li>
   <li><a href="#downloading-from-ncbi" id="toc-downloading-from-ncbi" class="nav-link" data-scroll-target="#downloading-from-ncbi">Downloading from NCBI</a></li>
   <li><a href="#listing-files" id="toc-listing-files" class="nav-link" data-scroll-target="#listing-files">Listing files</a></li>
   <li><a href="#decompressing-using-gzip" id="toc-decompressing-using-gzip" class="nav-link" data-scroll-target="#decompressing-using-gzip">Decompressing using <code>gzip</code></a></li>
   <li><a href="#importing-the-files-into-r" id="toc-importing-the-files-into-r" class="nav-link" data-scroll-target="#importing-the-files-into-r">Importing the files into R</a></li>
   <li><a href="#data-processing" id="toc-data-processing" class="nav-link" data-scroll-target="#data-processing">Data processing</a></li>
-  </ul>
-</li>
   </ul><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/demo-genome-searching.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
 <!-- main -->
@@ -307,8 +302,19 @@ <h1 class="title d-none d-lg-block">
   </div>
   
 
-</header><section id="challenge" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+</header><div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your profesor is interested on knowing how many complete genomes of Bacillus subtilis are there in the NCBI databases. He ask you later to count the number of features (genes, CDS, ncRNA, rRNA, etc.) in the genome of Bacillus subtilis NCIB 3610 (GCF_002055965.1). And tell you to document each of the steps and how did you end up with the answer. Saving the file with your initials (e.g., CG-activity01.{md,txt,docx})</p>
+</div>
+</div>
 <section id="downloading-a-genome" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="downloading-a-genome">Downloading a genome</h3>
 <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">ncbi-genome-download</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="downloading-from-ncbi" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="downloading-from-ncbi">Downloading from NCBI</h3>
@@ -335,7 +341,7 @@ <h1 class="title d-none d-lg-block">
 </section>
 </div>
 </section><section id="importing-the-files-into-r" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="importing-the-files-into-r">Importing the files into R</h3>
-<div class="cell" data-warclass-warning="false" data-warattr-warning="false">
+<div class="cell" data-warclass-warning="false" data-warattr-warning="false" data-hash="demo-genome-searching_cache/html/file-reading_99207958b71348f644a376668f84e5aa">
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyverse.tidyverse.org">tidyverse</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://fs.r-lib.org">fs</a></span><span class="op">)</span>
 
@@ -375,7 +381,7 @@ <h1 class="title d-none d-lg-block">
 </div>
 </div>
 </section><section id="data-processing" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="data-processing">Data processing</h3>
-<div class="cell">
+<div class="cell" data-hash="demo-genome-searching_cache/html/data-processing_91bdbc4dd42bab566973aec10221dbcd">
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="va">all_features_grouped</span> <span class="op">&lt;-</span> <span class="va">all_features</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html">rename</a></span><span class="op">(</span>feature <span class="op">=</span> <span class="va">`# feature`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">assembly</span>, <span class="va">feature</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
@@ -390,7 +396,7 @@ <h1 class="title d-none d-lg-block">
 <p>create a new dataset that will group by features per accession. get read of the weird name of the column. Select these two columns. Group by these two columns to perform. count the numbers of rows based on the applied group. generate a wide dataset sending row names as columns. Arrange descending by the number of CDSs.</p>
 
 
-</section></section></main><!-- /main --><script type="application/javascript">
+</section></main><!-- /main --><script type="application/javascript">
 window.document.addEventListener("DOMContentLoaded", function (event) {
   const disableStylesheet = (stylesheets) => {
     for (let i=0; i < stylesheets.length; i++) {
diff --git a/docs/demo-phylogenetics.html b/docs/demo-phylogenetics.html
index 9310e12..a2c88ce 100644
--- a/docs/demo-phylogenetics.html
+++ b/docs/demo-phylogenetics.html
@@ -272,8 +272,7 @@ <h1 class="quarto-secondary-nav-title">
         <nav id="TOC" role="doc-toc"><h2 id="toc-title">Table of contents</h2>
    
   <ul>
-<li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#sequence-alignment-cytb" id="toc-sequence-alignment-cytb" class="nav-link" data-scroll-target="#sequence-alignment-cytb">Sequence alignment <em>cytb</em></a></li>
+<li><a href="#sequence-alignment-cytb" id="toc-sequence-alignment-cytb" class="nav-link active" data-scroll-target="#sequence-alignment-cytb">Sequence alignment <em>cytb</em></a></li>
   <li><a href="#evolutionary-substitution-model" id="toc-evolutionary-substitution-model" class="nav-link" data-scroll-target="#evolutionary-substitution-model">Evolutionary substitution model</a></li>
   <li>
 <a href="#maximum-likelihood-reconstruction" id="toc-maximum-likelihood-reconstruction" class="nav-link" data-scroll-target="#maximum-likelihood-reconstruction">Maximum likelihood reconstruction</a>
@@ -311,9 +310,20 @@ <h1 class="title d-none d-lg-block">
   </div>
   
 
-</header><section id="challenge" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+</header><div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor has been working with some mammal species and want to know the relationships of some sampled individuals. To do so he extracted the DNA and amplified the mitochondrial CYTB gene of those individuals. He gives a folder with multiple sequences and ask you to align them and to reconstruct two trees one using maximum likelihood (ML) and other using a Bayesian inference (BI). Then ask you to explain if both trees are congruent with each other.</p>
-</section><section id="sequence-alignment-cytb" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="sequence-alignment-cytb">Sequence alignment <em>cytb</em>
+</div>
+</div>
+<section id="sequence-alignment-cytb" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="sequence-alignment-cytb">Sequence alignment <em>cytb</em>
 </h2>
 <div class="sourceCode" id="cb1"><pre class="sourceCode zsh code-with-copy"><code class="sourceCode zsh"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">linsi</span> <span class="at">--preservecase</span> <span class="at">--reorder</span> cytB.fasta <span class="op">&gt;</span> cytB-aligned.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="evolutionary-substitution-model" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="evolutionary-substitution-model">Evolutionary substitution model</h2>
@@ -322,10 +332,10 @@ <h1 class="title d-none d-lg-block">
 </section><section id="maximum-likelihood-reconstruction" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="maximum-likelihood-reconstruction">Maximum likelihood reconstruction</h2>
 <div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">raxml-ng</span> <span class="at">--msa</span> cytB-aligned.fasta <span class="at">--model</span> GTR+I+G4</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <section id="tree-building" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="tree-building">Tree building</h3>
-<div class="cell">
+<div class="cell" data-hash="demo-phylogenetics_cache/html/unnamed-chunk-1_5f67f100fe84738a6334ee503853aa01">
 
 </div>
-<div class="cell" data-layout-align="center">
+<div class="cell" data-layout-align="center" data-hash="demo-phylogenetics_cache/html/unnamed-chunk-2_9a8627b847bc61523d91927402fcd53d">
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="va">raxml_data</span> <span class="op">&lt;-</span> <span class="fu">read.tree</span><span class="op">(</span><span class="st">"cytB-aligned.fasta.raxml.support"</span><span class="op">)</span>
 
 <span class="va">raxml_data</span><span class="op">$</span><span class="va">tip.label</span> <span class="op">&lt;-</span> <span class="fu">str_replace_all</span><span class="op">(</span><span class="va">raxml_data</span><span class="op">$</span><span class="va">tip.label</span>, <span class="st">"_"</span>, <span class="st">" "</span><span class="op">)</span>
diff --git a/docs/demo-reads-assessment.html b/docs/demo-reads-assessment.html
index b9ca11e..29288e1 100644
--- a/docs/demo-reads-assessment.html
+++ b/docs/demo-reads-assessment.html
@@ -298,8 +298,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">14</span>&nb
     <h2 id="toc-title">Table of contents</h2>
    
   <ul>
-  <li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#general-stats-from-fastq-files" id="toc-general-stats-from-fastq-files" class="nav-link" data-scroll-target="#general-stats-from-fastq-files">General stats from fastq files</a></li>
+  <li><a href="#general-stats-from-fastq-files" id="toc-general-stats-from-fastq-files" class="nav-link active" data-scroll-target="#general-stats-from-fastq-files">General stats from fastq files</a></li>
   <li><a href="#a-graphical-assessment-of-reads" id="toc-a-graphical-assessment-of-reads" class="nav-link" data-scroll-target="#a-graphical-assessment-of-reads">A graphical assessment of reads</a></li>
   </ul>
 <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/demo-reads-assessment.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
@@ -329,10 +328,19 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">14</span>&nbsp;
 
 </header>
 
-<section id="challenge" class="level2 unnumbered">
-<h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+<div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor challenges you to assembly a bacterial genome. He wants to know if an assembly using Illumina reads or Nanopore reads is better. The raw sequences for Illumina could be downloaded with the code SRR15634574. And the Nanopore raw reads with SRR15634573 here: https://sra-explorer.info. Choose at least on set and follow the instruction from the lecture to assemble the genome. Document each step and send to the professor the <code>assembly-{your-initials}.fasta</code>. You could form groups of max. 4 students.</p>
-</section>
+</div>
+</div>
 <section id="general-stats-from-fastq-files" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="general-stats-from-fastq-files">General stats from fastq files</h2>
 <p>A simple but fast cli to display the general stats from fastq is <code>seqfu</code></p>
diff --git a/docs/demo-sanger-processing.html b/docs/demo-sanger-processing.html
index b4b65fe..f8d428d 100644
--- a/docs/demo-sanger-processing.html
+++ b/docs/demo-sanger-processing.html
@@ -272,8 +272,7 @@ <h1 class="quarto-secondary-nav-title">
         <nav id="TOC" role="doc-toc"><h2 id="toc-title">Table of contents</h2>
    
   <ul>
-<li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#processing-a-single-.ab1-pair" id="toc-processing-a-single-.ab1-pair" class="nav-link" data-scroll-target="#processing-a-single-.ab1-pair">Processing a single <code>.ab1</code> pair</a></li>
+<li><a href="#processing-a-single-.ab1-pair" id="toc-processing-a-single-.ab1-pair" class="nav-link active" data-scroll-target="#processing-a-single-.ab1-pair">Processing a single <code>.ab1</code> pair</a></li>
   <li><a href="#processing-a-bulk-of-.ab1-files" id="toc-processing-a-bulk-of-.ab1-files" class="nav-link" data-scroll-target="#processing-a-bulk-of-.ab1-files">Processing a bulk of <code>.ab1</code> files</a></li>
   </ul><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/demo-sanger-processing.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
@@ -299,10 +298,21 @@ <h1 class="title d-none d-lg-block">
   </div>
   
 
-</header><section id="challenge" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+</header><div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor gives you a couple of .ab1 files of a 16S rRNA gene from an old project a student conducted. She tells you to process and analyse them using the Sanger sequence pipeline analysis. And as she doesn’t know from which species they belong, she ask you to identify the organism to whom it belongs by using the resulting consensus sequence. She finally reminds you to document each step of the process including the identification step.</p>
-</section><section id="processing-a-single-.ab1-pair" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="processing-a-single-.ab1-pair">Processing a single <code>.ab1</code> pair</h2>
-<div class="cell">
+</div>
+</div>
+<section id="processing-a-single-.ab1-pair" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="processing-a-single-.ab1-pair">Processing a single <code>.ab1</code> pair</h2>
+<div class="cell" data-hash="demo-sanger-processing_cache/html/single-sanger-processing_4aefe2a4ccd3f4bddecbc4d6bd0b9cec">
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">sangeranalyseR</span><span class="op">)</span>
 
 <span class="va">groEL</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/sangeranalyseR/man/SangerAlignment.html">SangerAlignment</a></span><span class="op">(</span>
@@ -324,7 +334,7 @@ <h1 class="title d-none d-lg-block">
 <span class="fu"><a href="https://rdrr.io/pkg/sangeranalyseR/man/qualityBasePlot-methods.html">qualityBasePlot</a></span><span class="op">(</span><span class="va">groEL</span><span class="op">)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="processing-a-bulk-of-.ab1-files" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="processing-a-bulk-of-.ab1-files">Processing a bulk of <code>.ab1</code> files</h2>
-<div class="cell">
+<div class="cell" data-hash="demo-sanger-processing_cache/html/bulk-sanger-processing_c4b72b6614b7ed2b884ef9f5f29a4e2d">
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://fs.r-lib.org">fs</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="http://purrr.tidyverse.org">purrr</a></span><span class="op">)</span>
 
diff --git a/docs/search.json b/docs/search.json
index 69d5c9c..20d3b4d 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -326,14 +326,14 @@
     "href": "demo-genome-searching.html",
     "title": "\n10  Genome searching\n",
     "section": "",
-    "text": "Your profesor is interested on knowing how many complete genomes of Bacillus subtilis are there in the NCBI databases. He ask you later to count the number of features (genes, CDS, ncRNA, rRNA, etc.) in the genome of Bacillus subtilis NCIB 3610 (GCF_002055965.1). And tell you to document each of the steps and how did you end up with the answer. Saving the file with your initials (e.g., CG-activity01.{md,txt,docx})\n\nncbi-genome-download\n\nThe first step in this journey is to download a bunch of sequences programatically. To do so, we will use the program ncbi-genome-download.\nYou could inspect all the options it provides, now we will set our command as the following:\n#| echo: true\n#| eval: true\nngd --genera \"Bacillus subtilis\"\\\n    -s refseq\\\n    -l complete\\\n    -o Data\\\n    --flat-output\\\n    --format features\\\n    -n bacteria\\\n    | head -n 10\n\nls Data | head -n 10\n\ngzip -d *\n\n\nls Data | head\n\n\n\n\nlibrary(tidyverse)\nlibrary(fs)\n\nall_features <- dir_ls(\"Data/\") %>% \n  map_df(read_tsv)\n\nall_features %>% \n  head()\n\n\n\nlibrary(tidyverse)\n\n── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──\n\n\n✔ ggplot2 3.3.5     ✔ purrr   0.3.4\n✔ tibble  3.1.6     ✔ dplyr   1.0.8\n✔ tidyr   1.2.0     ✔ stringr 1.4.0\n✔ readr   2.1.2     ✔ forcats 0.5.1\n\n\n── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──\n✖ dplyr::filter() masks stats::filter()\n✖ dplyr::lag()    masks stats::lag()\n\nlibrary(fs)\n\nall_features <- dir_ls(\"Data/\") %>% \n  map_df(read_tsv)\n\nall_features %>% \n  head()\n\n# A tibble: 0 × 0\n\n\n\n\n\nall_features_grouped <- all_features %>% \n  rename(feature = `# feature`) %>% \n  select(assembly, feature) %>% \n  group_by(assembly, feature) %>%  operations\n  count() %>% \n  pivot_wider(names_from = feature, values_from = n) %>% \n  arrange(desc(CDS))\n    \nall_features_grouped %>% \n  head()\n\ncreate a new dataset that will group by features per accession. get read of the weird name of the column. Select these two columns. Group by these two columns to perform. count the numbers of rows based on the applied group. generate a wide dataset sending row names as columns. Arrange descending by the number of CDSs."
+    "text": "Downloading a genome\nncbi-genome-download\nDownloading from NCBI\nThe first step in this journey is to download a bunch of sequences programatically. To do so, we will use the program ncbi-genome-download.\nYou could inspect all the options it provides, now we will set our command as the following:\n#| echo: true\n#| eval: true\nngd --genera \"Bacillus subtilis\"\\\n    -s refseq\\\n    -l complete\\\n    -o Data\\\n    --flat-output\\\n    --format features\\\n    -n bacteria\\\n    | head -n 10\nListing files\nls Data | head -n 10\nDecompressing using gzip\n\ngzip -d *\n\nSome files in our data dir\nls Data | head\n\n\nImporting the files into R\n\nlibrary(tidyverse)\nlibrary(fs)\n\nall_features <- dir_ls(\"Data/\") %>% \n  map_df(read_tsv)\n\nall_features %>% \n  head()\n\n\n\nlibrary(tidyverse)\n\n── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──\n\n\n✔ ggplot2 3.3.5     ✔ purrr   0.3.4\n✔ tibble  3.1.6     ✔ dplyr   1.0.8\n✔ tidyr   1.2.0     ✔ stringr 1.4.0\n✔ readr   2.1.2     ✔ forcats 0.5.1\n\n\n── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──\n✖ dplyr::filter() masks stats::filter()\n✖ dplyr::lag()    masks stats::lag()\n\nlibrary(fs)\n\nall_features <- dir_ls(\"Data/\") %>% \n  map_df(read_tsv)\n\nall_features %>% \n  head()\n\n# A tibble: 0 × 0\n\n\n\nData processing\n\nall_features_grouped <- all_features %>% \n  rename(feature = `# feature`) %>% \n  select(assembly, feature) %>% \n  group_by(assembly, feature) %>%  operations\n  count() %>% \n  pivot_wider(names_from = feature, values_from = n) %>% \n  arrange(desc(CDS))\n    \nall_features_grouped %>% \n  head()\n\ncreate a new dataset that will group by features per accession. get read of the weird name of the column. Select these two columns. Group by these two columns to perform. count the numbers of rows based on the applied group. generate a wide dataset sending row names as columns. Arrange descending by the number of CDSs."
   },
   {
     "objectID": "demo-sanger-processing.html",
     "href": "demo-sanger-processing.html",
     "title": "\n11  Sanger processing\n",
     "section": "",
-    "text": "Your professor gives you a couple of .ab1 files of a 16S rRNA gene from an old project a student conducted. She tells you to process and analyse them using the Sanger sequence pipeline analysis. And as she doesn’t know from which species they belong, she ask you to identify the organism to whom it belongs by using the resulting consensus sequence. She finally reminds you to document each step of the process including the identification step."
+    "text": "Challenge\n\n\n\nYour professor gives you a couple of .ab1 files of a 16S rRNA gene from an old project a student conducted. She tells you to process and analyse them using the Sanger sequence pipeline analysis. And as she doesn’t know from which species they belong, she ask you to identify the organism to whom it belongs by using the resulting consensus sequence. She finally reminds you to document each step of the process including the identification step."
   },
   {
     "objectID": "demo-sanger-processing.html#processing-a-single-.ab1-pair",
@@ -417,7 +417,7 @@
     "href": "demo-phylogenetics.html",
     "title": "\n13  Phylogenetic analysis\n",
     "section": "",
-    "text": "Your professor has been working with some mammal species and want to know the relationships of some sampled individuals. To do so he extracted the DNA and amplified the mitochondrial CYTB gene of those individuals. He gives a folder with multiple sequences and ask you to align them and to reconstruct two trees one using maximum likelihood (ML) and other using a Bayesian inference (BI). Then ask you to explain if both trees are congruent with each other."
+    "text": "Challenge\n\n\n\nYour professor has been working with some mammal species and want to know the relationships of some sampled individuals. To do so he extracted the DNA and amplified the mitochondrial CYTB gene of those individuals. He gives a folder with multiple sequences and ask you to align them and to reconstruct two trees one using maximum likelihood (ML) and other using a Bayesian inference (BI). Then ask you to explain if both trees are congruent with each other."
   },
   {
     "objectID": "demo-phylogenetics.html#sequence-alignment-cytb",
@@ -452,7 +452,7 @@
     "href": "demo-reads-assessment.html",
     "title": "14  Sequence reads assesment",
     "section": "",
-    "text": "Your professor challenges you to assembly a bacterial genome. He wants to know if an assembly using Illumina reads or Nanopore reads is better. The raw sequences for Illumina could be downloaded with the code SRR15634574. And the Nanopore raw reads with SRR15634573 here: https://sra-explorer.info. Choose at least on set and follow the instruction from the lecture to assemble the genome. Document each step and send to the professor the assembly-{your-initials}.fasta. You could form groups of max. 4 students."
+    "text": "Challenge\n\n\n\nYour professor challenges you to assembly a bacterial genome. He wants to know if an assembly using Illumina reads or Nanopore reads is better. The raw sequences for Illumina could be downloaded with the code SRR15634574. And the Nanopore raw reads with SRR15634573 here: https://sra-explorer.info. Choose at least on set and follow the instruction from the lecture to assemble the genome. Document each step and send to the professor the assembly-{your-initials}.fasta. You could form groups of max. 4 students."
   },
   {
     "objectID": "demo-reads-assessment.html#general-stats-from-fastq-files",
@@ -473,7 +473,7 @@
     "href": "demo-genome-assembly.html",
     "title": "15  Genome assembly",
     "section": "",
-    "text": "Your professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs. sequence lengths (log transformed) and ii) the read length vs. read quality vs. read number.\nHe ask you to document every step and to conclude what data should be used."
+    "text": "Challenge\n\n\n\nYour professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs. sequence lengths (log transformed) and ii) the read length vs. read quality vs. read number.\nHe ask you to document every step and to conclude what data should be used."
   },
   {
     "objectID": "demo-genome-assembly.html#download-the-reads",
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index 09cb9b2..4e92f91 100644
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