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diff --git a/2023.11/.DS_Store b/2023.11/.DS_Store
diff --git a/2023.11/assets/pdf/01_introduction.pdf b/2023.11/assets/pdf/01_introduction.pdf
diff --git a/...11/assets/pdf/sequencing_technologies.pdf → ...assets/pdf/02_sequencing_technologies.pdf b/...11/assets/pdf/sequencing_technologies.pdf → ...assets/pdf/02_sequencing_technologies.pdf
diff --git a/2023.11/assets/pdf/reproducible_research.pdf → ...1/assets/pdf/03_reproducible_research.pdf b/2023.11/assets/pdf/reproducible_research.pdf → ...1/assets/pdf/03_reproducible_research.pdf
diff --git a/2023.11/assets/pdf/quality_control.pdf → 2023.11/assets/pdf/04_quality_control.pdf b/2023.11/assets/pdf/quality_control.pdf → 2023.11/assets/pdf/04_quality_control.pdf
diff --git a/2023.11/assets/pdf/read_alignment.pdf → 2023.11/assets/pdf/05_read_alignment.pdf b/2023.11/assets/pdf/read_alignment.pdf → 2023.11/assets/pdf/05_read_alignment.pdf
diff --git a/2023.11/assets/pdf/file_types.pdf → 2023.11/assets/pdf/06_file_types.pdf b/2023.11/assets/pdf/file_types.pdf → 2023.11/assets/pdf/06_file_types.pdf
diff --git a/2023.11/assets/pdf/group_work.pdf → 2023.11/assets/pdf/07_group_work.pdf b/2023.11/assets/pdf/group_work.pdf → 2023.11/assets/pdf/07_group_work.pdf
diff --git a/2023.11/assets/pdf/introduction.pdf b/2023.11/assets/pdf/introduction.pdf
diff --git a/2023.11/day1/intro/index.html b/2023.11/day1/intro/index.html
@@ -605,7 +605,7 @@ <h1>Introduction</h1>
 <p>If you are doing this course independently, you can skip this part.</p>
 </div>
 <h2 id="material">Material</h2>
-<p><a class="md-button" href="../../assets/pdf/introduction.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
+<p><a class="md-button" href="../../assets/pdf/01_introduction.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
 
 
 

diff --git a/2023.11/day1/quality_control/index.html b/2023.11/day1/quality_control/index.html
@@ -692,7 +692,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
 <h2 id="material">Material</h2>
 <iframe width="560" height="315" src="https://www.youtube.com/embed/iCOF6yaQFPE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
 
-<p><a class="md-button" href="../../assets/pdf/quality_control.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
+<p><a class="md-button" href="../../assets/pdf/04_quality_control.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
 <ul>
 <li><code>fastqc</code> command line <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt">documentation</a></li>
 <li><code>cutadapt</code> <a href="https://cutadapt.readthedocs.io/en/stable/">manual</a></li>

diff --git a/2023.11/day1/reproducibility/index.html b/2023.11/day1/reproducibility/index.html
@@ -647,7 +647,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
 <li>Apply some basic rules to support reproducibilty in computational research</li>
 </ul>
 <h2 id="material">Material</h2>
-<p><a class="md-button" href="../../assets/pdf/reproducible_research.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
+<p><a class="md-button" href="../../assets/pdf/03_reproducible_research.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
 <h3 id="some-good-practices-for-reproducibility">Some good practices for reproducibility</h3>
 <p>During today and tomorrow we will work with a small <em>E. coli</em> dataset to practice quality control, alignment and alignment filtering. You can consider this as a small project. During the exercise you will be guided to adhere to the following basic principles for reproducibility:</p>
 <ol>

diff --git a/2023.11/day1/sequencing_technologies/index.html b/2023.11/day1/sequencing_technologies/index.html
@@ -626,7 +626,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
 <h2 id="material">Material</h2>
 <iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLoCxWrRWjqB1VlFIdm0DCv9uKv7y-YuEE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
 
-<p><a class="md-button" href="../../assets/pdf/sequencing_technologies.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
+<p><a class="md-button" href="../../assets/pdf/02_sequencing_technologies.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
 <p><a href="https://www.youtube.com/watch?v=fCd6B5HRaZ8">Illumina sequencing by synthesis on YouTube</a></p>
 <p><a href="https://international.neb.com/applications/ngs-sample-prep-and-target-enrichment/-/media/nebus/files/brochures/nebnext_poster.pdf">NEBnext library preparation poster</a></p>
 

diff --git a/2023.11/day2/file_types/index.html b/2023.11/day2/file_types/index.html
@@ -629,7 +629,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
 <h2 id="material">Material</h2>
 <iframe width="560" height="315" src="https://www.youtube.com/embed/Y7syJJTPrSU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
 
-<p><a class="md-button" href="../../assets/pdf/file_types.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
+<p><a class="md-button" href="../../assets/pdf/06_file_types.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
 <p>File definition websites:</p>
 <ul>
 <li><a href="https://en.wikipedia.org/wiki/FASTQ_format">FASTQ (wikipedia)</a></li>

diff --git a/2023.11/day2/read_alignment/index.html b/2023.11/day2/read_alignment/index.html
@@ -679,7 +679,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
 <h2 id="material">Material</h2>
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 <ul>
 <li>Unix command line <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/">E-utilities documentation</a></li>
 <li><code>bowtie2</code> <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line">manual</a></li>