Commit e14fd2da authored by Laros's avatar Laros
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Added new lecture.

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# 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 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.
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\author{Jeroen F.J. Laros}
\title{\LaTeX\ Presentation Template}
\providecommand{\myConference}{Work discussion}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
% This disables the \pause command, handy in the editing phase.
% Make the title slide.
% First page of the presentation.
\section{Short introduction}
\subsection{Titles and subtitles}
Notice the title and subtitle:
\item The \emph{section} command controls the title.
\item The \emph{subsection} command controls the frametitle.
Testing \hl{highlight}\ colour.
The titles are retained until overwritten.
Notice the footer is present on all overlays.
\section{New section title which is rather long}
A \emph{pframe} does not need to be declared fragile.
\begin{lstlisting}[caption={Example input}]
print "Hello"
\subsection{Two columns}
\caption{Some picture.}
Sometimes it is convenient to have two columns.
\item Pictures can be too high.
\item You may have multiple small pictures.
\item \ldots
% Make the acknowledgements slide.
\bf Department one & \bf Other department\\
Colleague one & Someone\\
Colleague two & Someone else\\
Colleague three & Someone's supervisor\\
\includegraphics[height=1cm]{logos/lumc_logo_small} &
\includegraphics[height=1cm]{logos/ul_logo_white} &
\includegraphics[height=1cm]{logos/lumc_logo_small} &
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