diff --git a/grp_for_data_analysis/Makefile b/grp_for_data_analysis/Makefile
new file mode 120000
index 0000000000000000000000000000000000000000..199dff7226a84dcdd0c281699009a50ee16432d5
--- /dev/null
+++ b/grp_for_data_analysis/Makefile
@@ -0,0 +1 @@
+../presentation/Makefile
\ No newline at end of file
diff --git a/grp_for_data_analysis/beamerthemelumc.sty b/grp_for_data_analysis/beamerthemelumc.sty
new file mode 120000
index 0000000000000000000000000000000000000000..999deb4e197ab5cd127d06a12d63c324f88ec711
--- /dev/null
+++ b/grp_for_data_analysis/beamerthemelumc.sty
@@ -0,0 +1 @@
+../presentation/beamerthemelumc.sty
\ No newline at end of file
diff --git a/grp_for_data_analysis/gen2phen_logo.eps b/grp_for_data_analysis/gen2phen_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..0f2636661f1c186560f22691e6a5172e1bc3f7a8
--- /dev/null
+++ b/grp_for_data_analysis/gen2phen_logo.eps
@@ -0,0 +1 @@
+../presentation/gen2phen_logo.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/grp_for_data_analysis.tex b/grp_for_data_analysis/grp_for_data_analysis.tex
new file mode 100644
index 0000000000000000000000000000000000000000..075f8aa5b0d8014b2318baf79900547bec342ec0
--- /dev/null
+++ b/grp_for_data_analysis/grp_for_data_analysis.tex
@@ -0,0 +1,65 @@
+\documentclass[slidestop]{beamer}
+
+\title{Phylogenetic reconstruction}
+\providecommand{\myConference}{NGS introduction}
+\providecommand{\myDate}{Thursday, 22 May 2014}
+\author{Michiel van Galen}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+% First page of the presentation.
+\section{Introduction}
+\subsection{Some slide}
+\begin{pframe}
+   
+  \begin{itemize}
+    \item The \emph{section} command controls the title.
+    \item The \emph{subsection} command controls the frametitle.
+  \end{itemize}
+\end{pframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{pframe}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Jeroen Laros
+    \bigskip
+
+    Martijn Vermaat
+    \bigskip
+
+    Jeroen Frank
+    \bigskip
+
+    LGTC    
+
+  \end{center}
+\end{pframe}
+
+\end{document}
diff --git a/grp_for_data_analysis/lgtc_logo.eps b/grp_for_data_analysis/lgtc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..1732a7e9e5917e6840c9e5977fcff78334758d07
--- /dev/null
+++ b/grp_for_data_analysis/lgtc_logo.eps
@@ -0,0 +1 @@
+../presentation/lgtc_logo.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/lumc_logo.eps b/grp_for_data_analysis/lumc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..28075f649e2e97c354f0edcb8499aaa716802566
--- /dev/null
+++ b/grp_for_data_analysis/lumc_logo.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/lumc_logo_small.eps b/grp_for_data_analysis/lumc_logo_small.eps
new file mode 120000
index 0000000000000000000000000000000000000000..a5544fe55e1326788ad0ab37c560dc40c9adf29e
--- /dev/null
+++ b/grp_for_data_analysis/lumc_logo_small.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo_small.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/nbic_logo.eps b/grp_for_data_analysis/nbic_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..8780a0131e16e899fa17c12d886c4135f36e933d
--- /dev/null
+++ b/grp_for_data_analysis/nbic_logo.eps
@@ -0,0 +1 @@
+../presentation/nbic_logo.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/ngi_logo.eps b/grp_for_data_analysis/ngi_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..2a2e1ea9b13da5f50916f33c34e8b5607022962d
--- /dev/null
+++ b/grp_for_data_analysis/ngi_logo.eps
@@ -0,0 +1 @@
+../presentation/ngi_logo.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/nwo_logo_en.eps b/grp_for_data_analysis/nwo_logo_en.eps
new file mode 120000
index 0000000000000000000000000000000000000000..adcf12fd16e511dbe8213f21ba684611f13291bf
--- /dev/null
+++ b/grp_for_data_analysis/nwo_logo_en.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_en.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/nwo_logo_nl.eps b/grp_for_data_analysis/nwo_logo_nl.eps
new file mode 120000
index 0000000000000000000000000000000000000000..67830c9ef8ee053f74c8510ac87c2e8a4a4f88dc
--- /dev/null
+++ b/grp_for_data_analysis/nwo_logo_nl.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_nl.eps
\ No newline at end of file
diff --git a/grp_for_data_analysis/ul_logo.eps b/grp_for_data_analysis/ul_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..cd04dcb9c72ebdde50fda7ee41e375e053fc31b9
--- /dev/null
+++ b/grp_for_data_analysis/ul_logo.eps
@@ -0,0 +1 @@
+../presentation/ul_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/Makefile b/phylogenetic_reconstruction/Makefile
new file mode 120000
index 0000000000000000000000000000000000000000..199dff7226a84dcdd0c281699009a50ee16432d5
--- /dev/null
+++ b/phylogenetic_reconstruction/Makefile
@@ -0,0 +1 @@
+../presentation/Makefile
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/beamerthemelumc.sty b/phylogenetic_reconstruction/beamerthemelumc.sty
new file mode 120000
index 0000000000000000000000000000000000000000..999deb4e197ab5cd127d06a12d63c324f88ec711
--- /dev/null
+++ b/phylogenetic_reconstruction/beamerthemelumc.sty
@@ -0,0 +1 @@
+../presentation/beamerthemelumc.sty
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/clusterall_bw.ps b/phylogenetic_reconstruction/clusterall_bw.ps
new file mode 120000
index 0000000000000000000000000000000000000000..6c6991fd9c2e19d7e4e5323b286333741a2d0d33
--- /dev/null
+++ b/phylogenetic_reconstruction/clusterall_bw.ps
@@ -0,0 +1 @@
+../presentation-pics/pics/clusterall_bw.ps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/gen2phen_logo.eps b/phylogenetic_reconstruction/gen2phen_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..0f2636661f1c186560f22691e6a5172e1bc3f7a8
--- /dev/null
+++ b/phylogenetic_reconstruction/gen2phen_logo.eps
@@ -0,0 +1 @@
+../presentation/gen2phen_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/lgtc_logo.eps b/phylogenetic_reconstruction/lgtc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..1732a7e9e5917e6840c9e5977fcff78334758d07
--- /dev/null
+++ b/phylogenetic_reconstruction/lgtc_logo.eps
@@ -0,0 +1 @@
+../presentation/lgtc_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/lumc_logo.eps b/phylogenetic_reconstruction/lumc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..28075f649e2e97c354f0edcb8499aaa716802566
--- /dev/null
+++ b/phylogenetic_reconstruction/lumc_logo.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/lumc_logo_small.eps b/phylogenetic_reconstruction/lumc_logo_small.eps
new file mode 120000
index 0000000000000000000000000000000000000000..a5544fe55e1326788ad0ab37c560dc40c9adf29e
--- /dev/null
+++ b/phylogenetic_reconstruction/lumc_logo_small.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo_small.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/nbic_logo.eps b/phylogenetic_reconstruction/nbic_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..8780a0131e16e899fa17c12d886c4135f36e933d
--- /dev/null
+++ b/phylogenetic_reconstruction/nbic_logo.eps
@@ -0,0 +1 @@
+../presentation/nbic_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/ngi_logo.eps b/phylogenetic_reconstruction/ngi_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..2a2e1ea9b13da5f50916f33c34e8b5607022962d
--- /dev/null
+++ b/phylogenetic_reconstruction/ngi_logo.eps
@@ -0,0 +1 @@
+../presentation/ngi_logo.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/nwo_logo_en.eps b/phylogenetic_reconstruction/nwo_logo_en.eps
new file mode 120000
index 0000000000000000000000000000000000000000..adcf12fd16e511dbe8213f21ba684611f13291bf
--- /dev/null
+++ b/phylogenetic_reconstruction/nwo_logo_en.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_en.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/nwo_logo_nl.eps b/phylogenetic_reconstruction/nwo_logo_nl.eps
new file mode 120000
index 0000000000000000000000000000000000000000..67830c9ef8ee053f74c8510ac87c2e8a4a4f88dc
--- /dev/null
+++ b/phylogenetic_reconstruction/nwo_logo_nl.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_nl.eps
\ No newline at end of file
diff --git a/phylogenetic_reconstruction/phylogenetic_reconstruction.tex b/phylogenetic_reconstruction/phylogenetic_reconstruction.tex
new file mode 100644
index 0000000000000000000000000000000000000000..2a19d7d428a97a743ae7f56f98e96d118eadc101
--- /dev/null
+++ b/phylogenetic_reconstruction/phylogenetic_reconstruction.tex
@@ -0,0 +1,207 @@
+\documentclass[slidestop]{beamer}
+\title{Phylogenetic reconstruction}
+\providecommand{\myConference}{NGS introduction}
+\providecommand{\myDate}{Thursday, 22 May 2014}
+\author{Michiel van Galen}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+% First page of the presentation.
+\section{Material}
+\subsection{Input and goal}
+\begin{pframe}
+  \begin{itemize}
+    \item Sequence data available for different strains of bacteria
+    \item One FastQ file per strain
+  \end{itemize}
+    \bigskip
+
+    NGS throughput is much higher compared to conventional methods (Sanger
+sequencing). Increasing the chances on new insights.
+    \bigskip
+    
+    However, there is little solutions available to accommodate the magnitude in
+the field of phylogenetic reconstruction.
+\end{pframe}
+
+\section{Methods}
+\subsection{Naive approach}
+\begin{pframe}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.75\textwidth]{previous}
+  \end{figure}
+\end{pframe}
+
+\subsection{Naive approach}
+\begin{pframe}
+  Early workflow adapted from Sanger suffered from some limitations:
+  \bigskip
+
+  \begin{itemize}
+    \item Difficult to reproduce
+    \item Poorly documented
+    \item Using unconventional methods 
+    \item Not parallelized
+    \item Susceptible to errors
+    \item Customization or modification nearly impossible
+    \item Stops at the tree construction
+  \end{itemize}
+\end{pframe}
+
+\subsection{From bundle of scripts to pipeline}
+\begin{pframe}
+  Re-factor the workflow into a complete pipeline
+  \bigskip
+
+  \begin{itemize}
+    \item Convert the workflow to an automated pipeline
+    \item Replace custom scripts with maintained existing tools and methods
+    \item Include cluster support
+    \item Improve usability and customization 
+  \end{itemize}
+\end{pframe}
+
+\section{Pipeline}
+\subsection{Breakdown of the pipeline}
+\begin{pframe}
+  The workflow can be roughly broken down into two parts
+  \bigskip
+  
+  \begin{itemize}
+    \item Per sample part - Analyze the samples separately
+    \item Merged part - Combine output for each sample
+  \end{itemize}
+\end{pframe}
+
+\subsection{Per sample part}
+\begin{pframe}
+  These steps are for each sample the same and can be parallelized
+  \begin{itemize}
+    \item Add QC - Standard tools
+    \item Alignment to canonical reference - BWA
+    \item Variant calling and filtering - Samtools
+    \item Mask variants in repeated regions - BEDtools
+  \end{itemize}
+\end{pframe}
+
+\subsection{Merged part, combining the output}
+\begin{pframe}
+  \begin{itemize}
+    \item Compare the variants between strains - Python
+    \begin{itemize}
+      \item Merge the variant files into one matrix - VCFtools
+    \end{itemize}
+    \bigskip
+
+    \item Use PHYLIP to infer a evolutionary tree
+    \begin{itemize}
+      \item Create distance matrix (dnadist)
+      \item Create a phylogenetic tree
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Current situation}
+\subsection{Implementation}
+\begin{pframe}
+  The pipeline is designed to run on the LUMC Shark cluster
+  \begin{itemize}
+    \item All tools are available and maintained 
+    \item Pipeline is written in Make, compatible to run in parallel
+    \item Reduced the number of custom scripts to just one
+    \begin{itemize}
+      \item Not reinventing the wheel, outsource support for tools
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Future work}
+\subsection{Possible expansions}
+\begin{pframe}
+  \begin{itemize}
+    \item Improve usability even more
+    \begin{itemize}
+      \item User friendly interface 
+      \item More automation
+    \end{itemize}
+    \bigskip
+
+    \item kMer analysis
+    \begin{itemize}
+      \item Proven to work on meta-genomic datasets
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\subsection{kMer}
+\begin{pframe}
+  \begin{itemize}
+    \item Calculate distance between samples based on occurrences of words of length k
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.40\textwidth]{clusterall_bw.ps}
+  \end{figure}
+\end{pframe}
+
+\section{Conclusion}
+\begin{pframe}
+  Summarizing: 
+  \bigskip
+
+  \begin{itemize}
+    \item Much room for pipeline development and automation
+    \item Apply existing tools where possible reduce development time
+    \item Data is relatively small compared to human data making our
+    infrastructure well prepared
+  \end{itemize}
+\end{pframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{pframe}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Wilco Knetsch
+    \bigskip
+
+    Jeroen Laros
+    \bigskip
+
+    Martijn Vermaat
+    \bigskip
+
+    Jeroen Frank
+    \bigskip
+
+    LGTC    
+  \end{center}
+\end{pframe}
+
+\end{document}
diff --git a/phylogenetic_reconstruction/phylogenetic_reconstruction.tex.bak b/phylogenetic_reconstruction/phylogenetic_reconstruction.tex.bak
new file mode 100644
index 0000000000000000000000000000000000000000..e8046edb35b9de04b4aa1db3540d338ae9a0ba93
--- /dev/null
+++ b/phylogenetic_reconstruction/phylogenetic_reconstruction.tex.bak
@@ -0,0 +1,207 @@
+\documentclass[slidestop]{beamer}
+\title{Phylogenetic reconstruction}
+\providecommand{\myConference}{NGS introduction}
+\providecommand{\myDate}{Thursday, 22 May 2014}
+\author{Michiel van Galen}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+% First page of the presentation.
+\section{Material}
+\subsection{Input and goal}
+\begin{pframe}
+  \begin{itemize}
+    \item Sequence data available for different strains of bacteria
+    \item One FastQ file per strain
+  \end{itemize}
+    \bigskip
+
+    NGS throughput is much higher compared to conventional methods (Sanger
+sequencing). Increasing the chances on new insights.
+    \bigskip
+    
+    However, there is little solutions available to accomodate the magnitude in
+the field of phylogenetic reconstruction.
+\end{pframe}
+
+\section{Methods}
+\subsection{Naive approach}
+\begin{pframe}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.75\textwidth]{previous}
+  \end{figure}
+\end{pframe}
+
+\subsection{Naive approach}
+\begin{pframe}
+  Early workflow adapted from Sanger suffered from some limitations:
+  \bigskip
+
+  \begin{itemize}
+    \item Difficult to reproduce
+    \item Poorly documented
+    \item Using unconventional methods 
+    \item Not parallelized
+    \item Susceptible to errors
+    \item Customization or modification nearly impossible
+    \item Stops at the tree construction
+  \end{itemize}
+\end{pframe}
+
+\subsection{From bundle of scripts to pipeline}
+\begin{pframe}
+  Refactor the workflow into a complete pipeline
+  \bigskip
+
+  \begin{itemize}
+    \item Convert the workflow to an automated pipeline
+    \item Replace custom scripts with maintained existing tools and methods
+    \item Include cluster support
+    \item Improve usability and customization 
+  \end{itemize}
+\end{pframe}
+
+\section{Pipeline}
+\subsection{Breakdown of the pipeline}
+\begin{pframe}
+  The workflow can be roughly broken down into two parts
+  \bigskip
+  
+  \begin{itemize}
+    \item Per sample part - Analyze the samples seperately
+    \item Merged part - Combine output for each sample
+  \end{itemize}
+\end{pframe}
+
+\subsection{Per sample part}
+\begin{pframe}
+  These steps are for each sample the same and can be parallelized
+  \begin{itemize}
+    \item Add QC - Standard tools
+    \item Alignment to canonical reference - BWA
+    \item Variant calling and filtering - Samtools
+    \item Mask variants in repeated regions - BEDtools
+  \end{itemize}
+\end{pframe}
+
+\subsection{Merged part, combining the output}
+\begin{pframe}
+  \begin{itemize}
+    \item Compare the variants between strains - Python
+    \begin{itemize}
+      \item Merge the variant files into one matrix - VCFtools
+    \end{itemize}
+    \bigskip
+
+    \item Use PHYLIP to infer a evolutionary tree
+    \begin{itemize}
+      \item Create distance matrix (dnadist)
+      \item Create a phylogenetic tree
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Current situation}
+\subsection{Implementation}
+\begin{pframe}
+  The pipeline is designed to run on the LUMC Shark cluster
+  \begin{itemize}
+    \item All tools are available and maintained 
+    \item Pipeline is written in Make, compatible to run in parallel
+    \item Reduced the number of custom scripts to just one
+    \begin{itemize}
+      \item Not reinventing the wheel, outsource support for tools
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Future work}
+\subsection{Possible expansions}
+\begin{pframe}
+  \begin{itemize}
+    \item Improve usabilty even more
+    \begin{itemize}
+      \item User friendly interface 
+      \item More automation
+    \end{itemize}
+    \bigskip
+
+    \item kMer analysis
+    \begin{itemize}
+      \item Proven to work on metagenomic datasets
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\subsection{kMer}
+\begin{pframe}
+  \begin{itemize}
+    \item Calculate distance between samples based on occurences of words of length k
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.40\textwidth]{clusterall_bw.ps}
+  \end{figure}
+\end{pframe}
+
+\section{Conclusion}
+\begin{pframe}
+  Summarizing: 
+  \bigskip
+
+  \begin{itemize}
+    \item Much room for pipeline development and automation
+    \item Apply existing tools where possible reduce development time
+    \item Data is relatively small compared to human data making our
+    infrastructure well prepared
+  \end{itemize}
+\end{pframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{pframe}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Wilco Knetsch
+    \bigskip
+
+    Jeroen Laros
+    \bigskip
+
+    Martijn Vermaat
+    \bigskip
+
+    Jeroen Frank
+    \bigskip
+
+    LGTC    
+  \end{center}
+\end{pframe}
+
+\end{document}
diff --git a/phylogenetic_reconstruction/previous.png b/phylogenetic_reconstruction/previous.png
new file mode 100644
index 0000000000000000000000000000000000000000..2ce6b948e06330ee81cbedfbdcdb8ec31de057d4
Binary files /dev/null and b/phylogenetic_reconstruction/previous.png differ
diff --git a/phylogenetic_reconstruction/ul_logo.eps b/phylogenetic_reconstruction/ul_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..cd04dcb9c72ebdde50fda7ee41e375e053fc31b9
--- /dev/null
+++ b/phylogenetic_reconstruction/ul_logo.eps
@@ -0,0 +1 @@
+../presentation/ul_logo.eps
\ No newline at end of file
diff --git a/quality_control/Makefile b/quality_control/Makefile
new file mode 120000
index 0000000000000000000000000000000000000000..199dff7226a84dcdd0c281699009a50ee16432d5
--- /dev/null
+++ b/quality_control/Makefile
@@ -0,0 +1 @@
+../presentation/Makefile
\ No newline at end of file
diff --git a/quality_control/adapter_sequencing.png b/quality_control/adapter_sequencing.png
new file mode 120000
index 0000000000000000000000000000000000000000..bfe79ed062e512378c5338fee817cd2ccbfd45a9
--- /dev/null
+++ b/quality_control/adapter_sequencing.png
@@ -0,0 +1 @@
+../presentation-pics/pics/adapter_sequencing.png
\ No newline at end of file
diff --git a/quality_control/beamerthemelumc.sty b/quality_control/beamerthemelumc.sty
new file mode 120000
index 0000000000000000000000000000000000000000..999deb4e197ab5cd127d06a12d63c324f88ec711
--- /dev/null
+++ b/quality_control/beamerthemelumc.sty
@@ -0,0 +1 @@
+../presentation/beamerthemelumc.sty
\ No newline at end of file
diff --git a/quality_control/garbage.jpg b/quality_control/garbage.jpg
new file mode 120000
index 0000000000000000000000000000000000000000..61a423cbb01cb64188a533e57b960af3f6aa0a7c
--- /dev/null
+++ b/quality_control/garbage.jpg
@@ -0,0 +1 @@
+../presentation-pics/pics/garbage-in-garbage-out.jpg
\ No newline at end of file
diff --git a/quality_control/gen2phen_logo.eps b/quality_control/gen2phen_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..0f2636661f1c186560f22691e6a5172e1bc3f7a8
--- /dev/null
+++ b/quality_control/gen2phen_logo.eps
@@ -0,0 +1 @@
+../presentation/gen2phen_logo.eps
\ No newline at end of file
diff --git a/quality_control/lgtc_logo.eps b/quality_control/lgtc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..1732a7e9e5917e6840c9e5977fcff78334758d07
--- /dev/null
+++ b/quality_control/lgtc_logo.eps
@@ -0,0 +1 @@
+../presentation/lgtc_logo.eps
\ No newline at end of file
diff --git a/quality_control/lumc_logo.eps b/quality_control/lumc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..28075f649e2e97c354f0edcb8499aaa716802566
--- /dev/null
+++ b/quality_control/lumc_logo.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo.eps
\ No newline at end of file
diff --git a/quality_control/lumc_logo_small.eps b/quality_control/lumc_logo_small.eps
new file mode 120000
index 0000000000000000000000000000000000000000..a5544fe55e1326788ad0ab37c560dc40c9adf29e
--- /dev/null
+++ b/quality_control/lumc_logo_small.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo_small.eps
\ No newline at end of file
diff --git a/quality_control/nbic_logo.eps b/quality_control/nbic_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..8780a0131e16e899fa17c12d886c4135f36e933d
--- /dev/null
+++ b/quality_control/nbic_logo.eps
@@ -0,0 +1 @@
+../presentation/nbic_logo.eps
\ No newline at end of file
diff --git a/quality_control/ngi_logo.eps b/quality_control/ngi_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..2a2e1ea9b13da5f50916f33c34e8b5607022962d
--- /dev/null
+++ b/quality_control/ngi_logo.eps
@@ -0,0 +1 @@
+../presentation/ngi_logo.eps
\ No newline at end of file
diff --git a/quality_control/nwo_logo_en.eps b/quality_control/nwo_logo_en.eps
new file mode 120000
index 0000000000000000000000000000000000000000..adcf12fd16e511dbe8213f21ba684611f13291bf
--- /dev/null
+++ b/quality_control/nwo_logo_en.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_en.eps
\ No newline at end of file
diff --git a/quality_control/nwo_logo_nl.eps b/quality_control/nwo_logo_nl.eps
new file mode 120000
index 0000000000000000000000000000000000000000..67830c9ef8ee053f74c8510ac87c2e8a4a4f88dc
--- /dev/null
+++ b/quality_control/nwo_logo_nl.eps
@@ -0,0 +1 @@
+../presentation/nwo_logo_nl.eps
\ No newline at end of file
diff --git a/quality_control/pretrimmed_qscores.png b/quality_control/pretrimmed_qscores.png
new file mode 120000
index 0000000000000000000000000000000000000000..5fe738b8450d4dd0ee4d30f4dffc386f3f0fc5d5
--- /dev/null
+++ b/quality_control/pretrimmed_qscores.png
@@ -0,0 +1 @@
+../presentation-pics/pics/pretrimmed_qscores.png
\ No newline at end of file
diff --git a/quality_control/quality_control.tex b/quality_control/quality_control.tex
new file mode 100644
index 0000000000000000000000000000000000000000..877b9000832f29eaa726f8d0b946b5e48a741138
--- /dev/null
+++ b/quality_control/quality_control.tex
@@ -0,0 +1,251 @@
+\documentclass[slidestop]{beamer}
+\title{Quality control}
+\providecommand{\myConference}{NGS introduction}
+\providecommand{\myDate}{Thursday, 22 May 2014}
+\author{Michiel van Galen}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+\section{Introduction}
+\subsection{Overview}
+\begin{pframe}
+  \begin{itemize}
+    \item Data and the flaws
+    \item Quality control basics
+    \item Tools and advanced methods
+  \end{itemize}
+\end{pframe}
+
+\subsection{The data}
+\begin{pframe}
+  \begin{itemize}
+    \item FastQ: Expanded two line Fasta format
+    \item Four lines per entry
+    \item Sequence and per base phred quality combined 
+    \item Beware of different score offsets
+  \end{itemize}
+  \begin{lstlisting}[caption={FastQ format}]
+    @SEQ_ID
+    GATTTGGGGTTCAAAGCAGTA
+    +
+    !''*((((***+))%%%++)(
+  \end{lstlisting}
+\end{pframe}
+
+\subsection{The flaws}
+\begin{pframe}
+  At any point from the start of the experiment until beginning analyses,
+  quality can be jeopardized.
+  \bigskip
+
+  \begin{itemize}
+    \item Gathering material and sample prep
+      \begin{itemize}
+        \item Contamination, degradation, sample swap
+      \end{itemize}
+    \item Sequencing
+      \begin{itemize}
+        \item Exhausted chemicals, technical issues
+      \end{itemize}
+    \item Data integrity
+      \begin{itemize}
+        \item File corruption 
+      \end{itemize}
+    \item Many other unexpected external factors
+  \end{itemize}
+\end{pframe}
+
+\subsection{The consequence}
+\begin{pframe}
+  \bigskip
+
+  Low quality greatly influences the downstream analyses. 
+  \bigskip
+
+  \begin{figure}
+    \caption{Garbage in garbage out}
+    \centering
+    \includegraphics[width=0.5\textwidth]{garbage}
+  \end{figure}
+\end{pframe}
+
+\section{Quality control basics}
+\subsection{Quality assessment}
+\begin{pframe}
+  \begin{itemize} 
+    \item FastQC: A quality control tool for high throughput sequence data.
+    \item Assess the quality of your data in a fastq file
+  \end{itemize}
+  \begin{figure}
+    \caption{FastQC}
+    \centering
+    \includegraphics[width=0.5\textwidth]{pretrimmed_qscores}
+  \end{figure}
+\end{pframe}
+
+\subsection{Data properties}
+\begin{pframe}
+  Properties which can indicate possible biases in your data:
+  \begin{itemize}
+    \item Quality scores - Higher is better
+    \item GC content - Expected vs observed
+    \item Duplication rate - Lower is usually better
+    \item N content - Less is more
+    \item Adapter contaminants - More adapter, less sample
+    \item kMer statistics - Expected vs observed
+  \end{itemize}
+\end{pframe}
+
+\subsection{Improving your data}
+\begin{pframe}
+  After identification of some issues, correction may be possible
+  \bigskip
+
+  \begin{itemize}
+    \item Low quality bases can be discarded
+    \item Adapter sequences can be removed 
+    \item Downstream analyses can be tailored to identified problems
+  \end{itemize}
+\end{pframe}
+
+\subsection{Quality trimming}
+\begin{pframe}
+  \begin{itemize}
+    \item Getting rid of low quality bases
+    \item Only want to maintain the high-quality bases 
+  \end{itemize}
+  \begin{lstlisting}[language=none, caption={}]
+    @Header
+    ACGTACGTACGT
+    +
+    !#II!JJJI##!
+
+    Will result in:
+    --GTACGTA---
+  \end{lstlisting}
+\end{pframe}
+
+\subsection{Clipping adapters}
+\begin{pframe}
+  \begin{itemize}
+    \item FastQC can identify adapter contaminants which can hamper later analyses
+    \item Specific tools can remove these specific sequences
+  \end{itemize}
+  \begin{figure}
+    \caption{Adapter Sequencing}
+    \centering
+    \includegraphics[width=0.8\textwidth]{adapter_sequencing}
+  \end{figure}
+\end{pframe}
+
+\subsection{Digital data quality}
+\begin{pframe}
+  Also digital date can be of low quality
+  \bigskip
+
+  \begin{itemize}
+    \item Hardware failure
+    \begin{itemize}
+      \item Data corruption, insufficient disk space
+    \end{itemize}
+    \item Human failure
+    \begin{itemize}
+      \item Sample swaps, unclear file names, incomplete copies
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Tools and advanced methods}
+\subsection{kMer analysis}
+\begin{pframe}
+  \begin{itemize}
+    \item Analyzing the frequencies of words of length K
+    \item Proven to detect all sorts of factors which influence the data
+    \begin{itemize}
+      \item Contamination, quality, duplication
+    \end{itemize}
+    \item Also used to determine sample complexity
+  \end{itemize}
+\end{pframe} 
+
+\subsection{Overview of tools}
+\begin{pframe}
+  \begin{itemize}
+    \item{Quality assessment}
+    \begin{itemize}
+      \item FastQC, kMer, QCDB
+    \end{itemize}
+    \item{Trimming}
+    \begin{itemize}
+      \item Sickle: A windowed adaptive trimming tool
+    \end{itemize}
+    \item{Adapter clipping}
+    \begin{itemize}
+      \item Cutadapt
+    \end{itemize}
+    \item{File integrity}
+    \begin{itemize}
+      \item Md5checksums, GRP
+    \end{itemize}
+  \end{itemize}
+\end{pframe}  
+
+\subsection{QC process}
+\begin{pframe}
+  Good QC practice can be performed following the next steps:
+  \begin{itemize}
+    \item Assess the quality of raw data
+    \item Identify possible factors that impact the data
+    \item Apply the tools to improve the data 
+    \item Assess the quality again and evaluate the results
+  \end{itemize}
+  \bigskip
+
+  Preferably this can be done in a precompiled pipeline
+\end{pframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{pframe}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Jeroen Laros
+    \bigskip
+
+    Martijn Vermaat
+    \bigskip
+
+    Jeroen Frank
+    \bigskip
+
+    LGTC    
+
+  \end{center}
+\end{pframe}
+
+\end{document}
diff --git a/quality_control/quality_control.tex.bak b/quality_control/quality_control.tex.bak
new file mode 100644
index 0000000000000000000000000000000000000000..5b3c16ab9ae58ca5fc863529b5c8627e0bd09d01
--- /dev/null
+++ b/quality_control/quality_control.tex.bak
@@ -0,0 +1,251 @@
+\documentclass[slidestop]{beamer}
+\title{Quality control}
+\providecommand{\myConference}{Work discussion}
+\providecommand{\myDate}{Thursday, 22 May 2014}
+\author{Michiel van Galen}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    %\includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+
+\section{Introduction}
+\subsection{Overview}
+\begin{pframe}
+  \begin{itemize}
+    \item Data and the flaws
+    \item Quality control basics
+    \item Tools and advanced methods
+  \end{itemize}
+\end{pframe}
+
+\subsection{The data}
+\begin{pframe}
+  \begin{itemize}
+    \item FastQ: Expanded two line Fasta format
+    \item Four lines per entry
+    \item Sequence and per base phred quality combined 
+    \item Beware of different score offsets
+  \end{itemize}
+  \begin{lstlisting}[caption={FastQ format}]
+    @SEQ_ID
+    GATTTGGGGTTCAAAGCAGTA
+    +
+    !''*((((***+))%%%++)(
+  \end{lstlisting}
+\end{pframe}
+
+\subsection{The flaws}
+\begin{pframe}
+  At any point from the start of the experiment until beginning analyses,
+  quality can be jeopardized.
+  \bigskip
+
+  \begin{itemize}
+    \item Gathering material and sample prep
+      \begin{itemize}
+        \item Contamination, degradation, sample swap
+      \end{itemize}
+    \item Sequencing
+      \begin{itemize}
+        \item Exhausted chemicals, technical issues
+      \end{itemize}
+    \item Data integrity
+      \begin{itemize}
+        \item File corruption 
+      \end{itemize}
+    \item Many other unexpected external factors
+  \end{itemize}
+\end{pframe}
+
+\subsection{The consequence}
+\begin{pframe}
+  \bigskip
+
+  Low quality greatly influences the downstream analyses. 
+  \bigskip
+
+  \begin{figure}
+    \caption{Garbage in garbage out}
+    \centering
+    \includegraphics[width=0.5\textwidth]{garbage}
+  \end{figure}
+\end{pframe}
+
+\section{Quality control basics}
+\subsection{Quality assessment}
+\begin{pframe}
+  \begin{itemize} 
+    \item FastQC: A quality control tool for high throughput sequence data.
+    \item Assess the quality of your data in a fastq file
+  \end{itemize}
+  \begin{figure}
+    \caption{FastQC}
+    \centering
+    \includegraphics[width=0.5\textwidth]{pretrimmed_qscores}
+  \end{figure}
+\end{pframe}
+
+\subsection{Data properties}
+\begin{pframe}
+  Properties which can indicate possible biases in your data:
+  \begin{itemize}
+    \item Quality scores - Higer is better
+    \item GC content - Expected vs observed
+    \item Duplication rate - Lower is usually better
+    \item N content - Less is more
+    \item Adapter contaminants - More adapter, less sample
+    \item kMer statistics - Expected vs observed
+  \end{itemize}
+\end{pframe}
+
+\subsection{Improving your data}
+\begin{pframe}
+  After identification of some issues, correction may be possible
+  \bigskip
+
+  \begin{itemize}
+    \item Low quality bases can be discarded
+    \item Adapter sequences can be removed 
+    \item Downstream analyses can be tailored to identified problems
+  \end{itemize}
+\end{pframe}
+
+\subsection{Quality trimming}
+\begin{pframe}
+  \begin{itemize}
+    \item Getting rid of low quality bases
+    \item Only want to maintain the high-quality bases 
+  \end{itemize}
+  \begin{lstlisting}[language=none, caption={}]
+    @Header
+    ACGTACGTACGT
+    +
+    !#II!JJJI##!
+
+    Will result in:
+    --GTACGTA---
+  \end{lstlisting}
+\end{pframe}
+
+\subsection{Clipping adapters}
+\begin{pframe}
+  \begin{itemize}
+    \item FastQC can identify adapter contaminants which can hamper later analyses
+    \item Specific tools can remove these specific sequences
+  \end{itemize}
+  \begin{figure}
+    \caption{Adapter Sequencing}
+    \centering
+    \includegraphics[width=0.8\textwidth]{adapter_sequencing}
+  \end{figure}
+\end{pframe}
+
+\subsection{Digital data quality}
+\begin{pframe}
+  Also digital date can be of low quality
+  \bigskip
+
+  \begin{itemize}
+    \item Hardware failure
+    \begin{itemize}
+      \item Data corruption, insufficient disk space
+    \end{itemize}
+    \item Human failure
+    \begin{itemize}
+      \item Sample swaps, unclear filenames, incomplete copies
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\section{Tools and advanced methods}
+\subsection{kMer analysis}
+\begin{pframe}
+  \begin{itemize}
+    \item Analyzing the frequencies of words of length K
+    \item Proven to detect all sorts of factors which influence the data
+    \begin{itemize}
+      \item Contamination, quality, duplication
+    \end{itemize}
+    \item Also used to determine sample complexity
+  \end{itemize}
+\end{pframe} 
+
+\subsection{Overview of tools}
+\begin{pframe}
+  \begin{itemize}
+    \item{Qualty assessment}
+    \begin{itemize}
+      \item FastQC, kMer, QCDB
+    \end{itemize}
+    \item{Trimming}
+    \begin{itemize}
+      \item Sickle: A windowed adaptive trimming tool
+    \end{itemize}
+    \item{Adapter clipping}
+    \begin{itemize}
+      \item Cutadapt
+    \end{itemize}
+    \item{File integrity}
+    \begin{itemize}
+      \item Md5checksums, GRP
+    \end{itemize}
+  \end{itemize}
+\end{pframe}  
+
+\subsection{QC process}
+\begin{pframe}
+  Good QC practice can be performed following the next steps:
+  \begin{itemize}
+    \item Assess the quality of raw data
+    \item Identify possible factors that impact the data
+    \item Apply the tools to improve the data 
+    \item Assess the quality again and evaluate the results
+  \end{itemize}
+  \bigskip
+
+  Preferably this can be done in a precompiled pipeline
+\end{pframe}
+
+\section{Questions?}
+\lastpagetemplate
+\begin{pframe}
+  \begin{center}
+    Acknowledgements:
+    \bigskip
+    \bigskip
+
+    Jeroen Laros
+    \bigskip
+
+    Martijn Vermaat
+    \bigskip
+
+    Jeroen Frank
+    \bigskip
+
+    LGTC    
+
+  \end{center}
+\end{pframe}
+
+\end{document}
diff --git a/quality_control/ul_logo.eps b/quality_control/ul_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..cd04dcb9c72ebdde50fda7ee41e375e053fc31b9
--- /dev/null
+++ b/quality_control/ul_logo.eps
@@ -0,0 +1 @@
+../presentation/ul_logo.eps
\ No newline at end of file