Added new lecture.

lectures/k_mer_long/Makefile

+../../submodules/presentation/Makefile
\ No newline at end of file

lectures/k_mer_long/abstract.md

+# Outline
+## Title
+Applications of k-mer profiling in genomics.
+
+## Abstract
+We describe a number of applications of a method that utilises profiles of
+k-mer frequencies made from raw sequencing data. This method was originally
+designed for the comparison of raw datasets without the need for a common
+reference sequence. Additionally, by analysis of the characteristics of the
+profile itself, technical artefacts, e.g., various problems with the sample
+preparation, contamination, etc., can be detected. Moreover, this method can be
+used for the deconvolution of metagenomic datasets. These datasets (mostly
+microbial communities) can be extremely complex as they can consist of several
+hundreds of species, many of which are unknown, so alignment free methods like
+ours are highly desired.
+
+## Sources
+### Paper abstract
+We describe an open-source kPAL package that facilitates an alignment-free
+assessment of the quality and comparability of sequencing datasets by analyzing
+k-mer frequencies. We show that kPAL can detect technical artefacts such as
+high duplication rates, library chimeras, contamination and differences in
+library preparation protocols. kPAL also successfully captures the complexity
+and diversity of microbiomes and provides a powerful means to study changes in
+microbial communities. Together, these features make kPAL an attractive and
+broadly applicable tool to determine the quality and comparability of sequence
+libraries even in the absence of a reference sequence. kPAL is freely available
+at https://github.com/LUMC/kPAL webcite.
+
+### Poster abstract
+Due to advances in sequencing technologies, the human microbiome is becoming an
+increasingly informative source for scientific researches. A proper comparison
+by deep analysis of skin bacterial communities would make a valuable
+contribution to many fields, notably forensics. The analysis of metagenomic
+samples usually involves mapping reads to known genes or pathways and comparing
+the obtained profiles. However, microbial communities are usually complex and
+contain mixtures of hundreds to thousands of unknown bacteria which affect the
+accuracy and completeness of alignment-based approaches. We developed an
+alignment-free approach (kPal [1]) that is based on k-mer frequencies to assess
+the level of similarity between and within metagenomic datasets. Previously our
+method was successfully applied for the comparison of different metagenomic
+samples. Recently we shown that k-mer based approach also can be utilized for
+classifying reads within a single metagenomic dataset. To illustrate this
+statement we used simulated and real data from a single molecule real time
+sequencer (PacBio) which provides long reads (500 - 20,000 bp). We have shown
+that k-mer frequencies can reveal the relationships between reads within a
+single metagenome, leading to a clustering per bacteria. This approach may
+potentially be used to estimate the metagenome complexity and to simplify the
+subsequent assembly procedure.

lectures/k_mer_long/beamerthemelumc.sty

+../../submodules/presentation/beamerthemelumc.sty
\ No newline at end of file

lectures/k_mer_long/k_mer_long.tex

+\documentclass[slidestop]{beamer}
+
+\author{Jeroen F.J. Laros}
+\title{\LaTeX\ Presentation Template}
+\providecommand{\mySubTitle}{Subtitle}
+\providecommand{\myConference}{Work discussion}
+\providecommand{\myDate}{12-nov-2015}
+\providecommand{\myGroup}{Leiden Genome Technology Center}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title slide.
+\makeTitleSlide{\includegraphics[height=3.5cm]{logos/lumc_logo_small}}
+
+% First page of the presentation.
+\section{Short introduction}
+\subsection{Titles and subtitles}
+\begin{pframe}
+  Notice the title and subtitle:
+  \begin{itemize}
+    \item The \emph{section} command controls the title.
+    \item The \emph{subsection} command controls the frametitle.
+  \end{itemize}
+  \bigskip
+
+  Testing \hl{highlight}\ colour.
+\end{pframe}
+
+\begin{pframe}
+  The titles are retained until overwritten.
+  \bigskip
+  \pause
+  
+  Notice the footer is present on all overlays.
+  \vfill
+  \permfoot{\url{https://git.lumc.nl/j.f.j.laros/presentation/tree/master}}
+\end{pframe}
+
+\section{New section title which is rather long}
+\subsection{Code}
+\begin{pframe}
+  A \emph{pframe} does not need to be declared fragile.
+
+  \begin{lstlisting}[caption={Example input}]
+    print "Hello"
+  \end{lstlisting}
+\end{pframe}
+
+\subsection{Two columns}
+\begin{pframe}
+  \begin{minipage}[t]{0.47\textwidth}
+    \begin{figure}
+      \begin{center}
+        \includegraphics[width=\textwidth]{logos/lumc_logo_small}
+      \end{center}
+      \caption{Some picture.}
+    \end{figure}
+  \end{minipage}
+  \hfill
+  \begin{minipage}[t]{0.47\textwidth}
+    Sometimes it is convenient to have two columns.
+    \begin{itemize}
+      \item Pictures can be too high.
+      \item You may have multiple small pictures.
+      \item \ldots
+    \end{itemize}
+  \end{minipage}
+\end{pframe}
+
+% Make the acknowledgements slide.
+\makeAcknowledgementsSlide{
+  \begin{tabular}{ll}
+    \bf Department one  & \bf Other department\\
+    Colleague one       & Someone\\
+    Colleague two       & Someone else\\
+    Colleague three     & Someone's supervisor\\
+    Supervisor\\
+  \end{tabular}
+  \bigskip
+
+  \begin{tabular}{llll}
+    \includegraphics[height=1cm]{logos/lumc_logo_small} &
+    \includegraphics[height=1cm]{logos/ul_logo_white} &
+    \includegraphics[height=1cm]{logos/lumc_logo_small} &
+    \includegraphics[height=1cm]{logos/ul_logo_white}
+  \end{tabular}
+}
+
+\end{document}

lectures/k_mer_long/logos

+../../submodules/presentation/logos
\ No newline at end of file