Replaced introduction with original one.

analysis_intro/Makefile

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analysis_intro/analysis.png

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analysis_intro/analysis_intro.tex

-\documentclass[slidestop]{beamer}
-
-\title{Introduction to NGS data analysis}
-\providecommand{\myConference}{NGS Introduction Course}
-\providecommand{\myDate}{Tuesday, 1 April 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 to NGS data analysis}
-\subsection{Introduction to NGS}
-\begin{pframe}
-  An introduction into NGS will be handled in the other lectures. 
-  However, ask us any questions you still may have.
-  \begin{figure}
-    \centering
-    \includegraphics[width=0.65\textwidth]{developments-in-ngs}
-  \end{figure}
-\end{pframe}
-
-\subsection{Introduction to data}
-\begin{pframe}
-  \begin{figure}
-    \centering
-    \includegraphics[width=0.77\textwidth]{data}
-  \end{figure}
-\end{pframe}
-
-\subsection{Introduction to analysis}
-\begin{pframe}
-  \begin{figure}
-    \centering
-    \includegraphics[width=0.74\textwidth]{analysis}
-  \end{figure}
-\end{pframe}
-
-% Section
-\section{About us and this course}
-\subsection{NGS activities in the LUMC}
-\begin{pframe}
-  LGTC, SASC, ServiceXS
-  \begin{itemize}
-    \item Data production and management
-    \item Development and maintenance of analysis pipelines
-  \end{itemize}
-  \bigskip
-
-  Wide range of different approaches and applications towards multiple purposes: 
-  \begin{itemize}
-    \item Fundamental research and clinical applications
-    \item Various technologies: HiSeq, MiSeq, Pacbio, Proton, etc.
-    \item Numerous techniques: DNA, RNA, capture, etc.
-    \item Diverse input: Humans, other animals, bacteria, etc.
-  \end{itemize}
-\end{pframe}
-
-\subsection{The focus of this course}
-\begin{pframe}
-  We will introduce you into the following areas:
-  \begin{itemize}
-    \item Operating systems (Linux)
-    \item Installing and maintaining your software
-    \item Starting NGS analysis
-    \item Using (remote) computer resources
-    \item Analysis pipelines
-  \end{itemize}
-\end{pframe}
-
-% Last section
-\section{Questions?}
-\lastpagetemplate
-\begin{pframe}
-  \begin{center}
-    \bigskip
-    \bigskip
-    \bigskip
-    \bigskip
-
-    Michiel van Galen
-
-    Jeroen Laros
-  \end{center}
-
-  \vfill
-  \permfoot{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/NGS-intro}
-\end{pframe}
-\end{document}

analysis_intro/beamerthemelumc.sty

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analysis_intro/data.png

-../presentation-pics/pics/data.png
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analysis_intro/developments-in-ngs.jpg

-../presentation-pics/pics/developments-in-ngs.jpg
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analysis_intro/gen2phen_logo.eps

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analysis_intro/lgtc_logo.eps

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analysis_intro/lumc_logo.eps

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analysis_intro/lumc_logo_small.eps

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analysis_intro/nbic_logo.eps

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analysis_intro/ngi_logo.eps

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analysis_intro/nwo_logo_en.eps

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analysis_intro/nwo_logo_nl.eps

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analysis_intro/ul_logo.eps

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introduction/Makefile

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introduction/beamerthemelumc.sty

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introduction/introduction.tex

+% LUMC presentation template by J. F. J. Laros.
+% Last alteration on 15-10-2009.
+%
+% The packages texlive-latex-recommended, texlive-latex-base and
+%   texlive-latex-extra should be installed.
+%
+
+% Alter these four lines for a new presentation.
+\providecommand{\me}{Michiel van Galen and Jeroen F. J. Laros}
+\providecommand{\myTitle}{General Introduction}
+\providecommand{\myConference}{NGS Introduction Course}
+\providecommand{\myDate}{Friday, 30 March 2012}
+
+% Now go to %%% BEGIN PRESENTATION %%%
+
+\documentclass[a4, portrait]{seminar}
+
+\usepackage{semcolor} % For coloured text.
+\usepackage{slidesec} % For section headings.
+\usepackage{newcent}  % This is a better font for presentations.
+\input{seminar.bug}
+
+\usepackage{graphicx} % For pictures.
+\usepackage{fancybox} % For the background picture.
+
+\definecolor{Blue}{rgb}{0.,0.11372,0.37647} % Custom LUMC color
+
+\renewcommand{\labelitemi}{\textcolor{white}{$\bullet$}} % Make the bullets for
+\renewcommand{\labelitemii}{\textcolor{white}{--}}       % itemising white.
+\renewcommand{\labelitemiii}{\textcolor{white}{$\ast$}}
+\renewcommand{\labelitemiv}{\textcolor{white}{$\circ$}}
+\renewcommand{\labelenumi}{\textcolor{white}{\arabic{enumi}.}}
+
+\newslideframe{TITLE}{ % Template for the title.
+  \boxput{
+    \rput(0, 0){\includegraphics[angle=90, scale=.485]{bg}}
+  }{#1}
+}
+
+\newslideframe{PRES}{ % Template for the body.
+  \boxput{
+    \rput(0, 0){\includegraphics[angle=90, scale=.485]{bg2}}
+  }{
+    \textcolor{Blue}{
+    \rput[l]{90}(8.57, -1.5){\scriptsize{\myConference}} 
+    \rput[c]{90}(8.57, 5.35){\scriptsize{\theslide/\pageref{LastPage}}}
+    \rput[r]{90}(8.57, 12.2){\scriptsize{\myDate}}
+    }
+    \white #1
+  }
+}
+
+\renewcommand{\makeslideheading}[1]{ % Put the slide headings on top.
+  \rput[l](0.2, .40){
+      \textbf{
+        \textcolor{Blue}{#1}
+    }
+  }
+  \newline
+}
+
+\pagestyle{empty}
+
+\begin{document}
+
+\slideframe{TITLE} % Use the title template.
+
+\begin{slide}
+  \setcounter{slide}{0}
+  \vspace*{1.5cm}
+  \begin{center}
+    {\bf\Large{\myTitle}}\\
+    \vfill
+    \textcolor{Blue}{
+      {\bf
+        \small{\me}\\
+        \small{Department of Human Genetics}\\
+        \small{Center for Human and Clinical Genetics}
+      }
+    }
+    \vspace{1.1cm}
+  \end{center}
+\end{slide}
+
+\slideframe{PRES} % Use the body template.
+
+%%% BEGIN PRESENTATION %%%
+
+\begin{slide}
+  \slideheading{Introduction}
+
+  A selection of the landmarks in sequencing.
+  \bigskip
+
+  \begin{tabular}{l|p{9cm}}
+    Year & Landmark\\
+    \hline
+    1953 & Discovery of the structure of the DNA double helix.\\
+    1977 & The first complete DNA genome sequenced ($\Phi$X174).\\
+    1986 & First semi-automated DNA sequencing machine.\\
+    1995 & First complete genome of a free-living organism.\\
+    2001 & A draft sequence of the human genome is published.\\
+    2004 & 454 Life Sciences markets a parallelized version of
+           \hbox{pyrosequencing}.\\
+  \end{tabular}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Next Generation Sequencing (NGS)}
+
+  High throughput parallel sequencing.
+  \begin{itemize}
+    \item Developed started in the 1990s.
+    \item Became available on the market in 2004.
+  \end{itemize}
+  \bigskip
+  \bigskip
+
+  Nowadays there are three major platforms available
+
+  \begin{itemize}
+    \item Solid sequencing.
+    \item 454 pyrosequencing.
+    \item Illumina (Solexa) sequencing.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Solid sequencing}
+
+  SOLiD: Sequencing by Oligonucleotide Ligation and Detection.
+
+  \begin{itemize}
+    \item Manufacturer: Life Technologies.
+    \item Commercially available since 2008.
+    \item Per cycle, $2$ bases are read.
+    \item Each base is read twice.
+  \end{itemize}
+  \bigskip
+
+  Pros:
+  \begin{itemize}
+    \item Single base read errors can be detected.
+  \end{itemize}
+  \bigskip
+
+  Cons:
+  \begin{itemize}
+    \item Software has to be adapted to work in \emph{colour space}.
+    \item The first nucleotide \emph{must} be known.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{454 pyrosequencing}
+
+  Long reads with the Roche 454.
+  
+  \begin{itemize}
+    \item Manufacturer: 454 Life Sciences (Roche).
+    \item Commercially available since 2005.
+    \item Per cycle, a variable number of bases are read (monomer stretches).
+    \item Used in forensic science.
+  \end{itemize}
+  \bigskip
+
+  Pros:
+  \begin{itemize}
+    \item Long reads ($400$-$500$ base pairs, $1000$ announced).
+  \end{itemize}
+  \bigskip
+
+  Cons:
+  \begin{itemize}
+    \item Deals poorly with monomer stretches.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Illumina (Solexa) sequencing}
+
+  The Illumina Genome Analyser II (GAII).
+
+  \begin{itemize}
+    \item Manufacturer: Illumina, Inc.
+    \item Commercially available since 2005.
+    \item Per cycle, one base is read.
+    \item Reads up to $100 \times 2$ base pairs.
+    \item Takes about $8$ days.
+    \item Produces about $40$ Giga bases per run.
+  \end{itemize}
+  \bigskip
+
+  Pros:
+  \begin{itemize}
+    \item Does paired end sequencing.
+    \item Cheap.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Illumina (Solexa) sequencing}
+
+  The Illumina HiSeq.
+
+  \begin{itemize}
+    \item Manufacturer: Illumina, Inc.
+    \item Commercially available since 2010.
+    \item Per cycle, one base is read.
+    \item Reads up to $150 \times 2$ base pairs.
+    \item Takes about $8$ days.
+    \item Produces about $150$ Giga bases per run.
+  \end{itemize}
+  \bigskip
+
+  Pros:
+  \begin{itemize}
+    \item Even higher throughput.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Sequencers at the LUMC}
+
+  We have the following sequencers at our disposal.
+  \bigskip
+
+  First generation, mainly used for short sequences and validation.
+  \begin{itemize}
+    \item $3$ Sanger sequencers: ($2 \times$ 3100 and 3730).
+  \end{itemize}
+  \bigskip
+
+  Next generation, high throughput.
+  \begin{itemize}
+    \item $2$ Illumina GAII.
+    \item $1$ Illumina HiSeq (got it last week).
+    \item $1$ Roche 454.
+  \end{itemize}
+  \bigskip
+
+  Next (and a half) generation.
+  \begin{itemize}
+    \item $1$ Helicos.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Paired end sequencing}
+
+  By sequencing two ends of a molecule, mapping can be improved.
+  \begin{itemize}
+    \item If one end maps more than once, the second end can be used to
+      uniquely determine the position.
+  \end{itemize}
+  \bigskip
+  
+  After the first read is done:
+  \begin{itemize}
+    \item Sequencing stops and chemicals are refreshed.
+    \item A second \emph{sequencing primer} is added.
+    \item The sequencer is started again.
+  \end{itemize}
+  \bigskip
+
+  Note that:
+  \begin{itemize}
+    \item It is very important that the flow cell is not moved.
+    \item Typically, the second read is shorter than the first one.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Barcoding}
+
+  Barcoding is a way to tag samples, in order for them to be pooled in one
+  lane.
+
+  Afterwards, we use the barcode to split the data.
+
+  \begin{itemize}
+    \item Usually added in the PCR step.
+    \item Designed in such a way, that single errors can be corrected.
+    \begin{itemize}
+      \item The \emph{edit distance} between two barcodes is at least three.
+      \item Introducing one error (insertion, deletion or substitution) will 
+        result in a edit distance of one.
+      \item Since the distance to other barcodes is still at least two, we 
+        can assign the barcode anyway.
+    \end{itemize}
+    \item Can be used as an additional quality control.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Helicos}
+
+  True single molecule sequencing.
+
+  Pros:
+  \begin{itemize}
+    \item No amplification.
+    \item Detection of mixed samples (forensics).
+  \end{itemize}
+  \bigskip
+
+  Cons:
+  \begin{itemize}
+    \item Short reads ($32$).
+    \item Suffers from \emph{dark nucleotides}.
+    \item Has a high error rate.
+    \item No barcoding.
+    \item No paired end (yet).
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Third generation sequencing}
+
+  Characteristics:
+  \begin{itemize}
+    \item Single molecule.
+    \item Long reads (several kilobases).
+  \end{itemize}
+  \bigskip
+
+  Applications:
+  \begin{itemize}
+    \item De novo assembly.
+  \end{itemize}
+  \bigskip
+
+  Companies:
+  \begin{itemize}
+    \item Pacific Bio.
+    \item Ion Torrent.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \slideheading{Outline}
+
+  We start with a basic introduction to Linux.
+  \begin{itemize}
+    \item Why do we use / need Linux?
+    \item Using the \emph{command line} and NGS tools (building blocks).
+    \item Connecting to other machines.
+  \end{itemize}
+  \bigskip
+
+  Furthermore, we focus on pipelines.
+  \begin{itemize}
+    \item Combine the building blocks into a pipeline.
+    \item Common pipelines.
+    \begin{itemize}
+      \item Variant detection.
+      \item Expression analysis.
+    \end{itemize}
+    \item Using \emph{Galaxy}.
+  \end{itemize}
+  \vfill
+\end{slide}
+
+\begin{slide}
+  \rput(5.4,0.7){\includegraphics[scale=0.07]{lgtc_logo}}
+  \rput(10.6,0.6){\includegraphics[scale=0.1]{nbic_logo}}
+  \slideheading{Questions?}
+
+  \bigskip
+  \bigskip
+  \bigskip
+  \begin{center}
+    Michiel van Galen\\
+    Jeroen Laros
+    \bigskip
+
+    \texttt{http://www.mutalyzer.nl/NGSIntroCourse/}
+  \end{center}
+  \vfill
+  \label{LastPage}
+\end{slide}
+
+\end{document}

introduction/logos

+../.submodules/presentation/logos
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