Updated lab-oriented NGS introduction.

lectures/intro_bio_ngs/intro_bio_ngs.tex

@@ -64,21 +64,6 @@
   \end{minipage}
 \end{pframe}
 
-%\begin{pframe}
-%  \begin{minipage}[t]{0.47\textwidth}
-%    \begin{figure}[]
-%      \begin{center}
-%        \includegraphics[width=\textwidth]{cromossomo_descondensando}
-%      \end{center}
-%      \caption{Chromosomes.}
-%    \end{figure}
-%  \end{minipage}
-%  \hfill
-%  \begin{minipage}[t]{0.47\textwidth}
-%    The nucleus contains \emph{chromosomes}.
-%  \end{minipage}
-%\end{pframe}
-
 \subsection{DNA}
 \begin{pframe}
   \begin{figure}[]
@@ -101,15 +86,6 @@
   \end{figure}
 \end{pframe}
 
-%\begin{pframe}
-%  \begin{figure}[]
-%    \begin{center}
-%      \includegraphics[width=\textwidth]{Simple_transcription_elongation1}
-%    \end{center}
-%    \caption{RNA synthesis.}
-%  \end{figure}
-%\end{pframe}
-
 \section{Sequencing}
 \subsection{DNA synthesis}
 \begin{pframe}
@@ -173,7 +149,7 @@
   Labelled:
   \begin{itemize}
     \item Optical platform.
-    \item In system amplification.
+    \item In system amplification to get enough signal.
   \end{itemize}
   \bigskip
 
@@ -196,6 +172,13 @@
   \end{minipage}
   \hfill
   \begin{minipage}[t]{0.47\textwidth}
+    In general:
+    \begin{itemize}
+      \item Fragmentation.
+      \item Adapter ligation.
+    \end{itemize}
+    \bigskip
+
     Y-adapters:
     \begin{itemize}
       \item No loss of sample.
@@ -210,10 +193,13 @@
 \begin{pframe}
   \begin{figure}[]
     \begin{center}
-      \includegraphics[width=\textwidth]{nextera}
+      \includegraphics[height=0.6\textheight]{nextera}
     \end{center}
-    \caption{Fragmentation and adapter ligation in one.}
+    \caption{Nextera.}
   \end{figure}
+
+  Fragmentation and adapter ligation in one step using a \emph{transposon}
+  based method.
 \end{pframe}
 
 \begin{pframe}
@@ -227,20 +213,23 @@
   \end{minipage}
   \hfill
   \begin{minipage}[t]{0.47\textwidth}
-    Capture \emph{coding regions} only.
+    Capture \emph{coding regions}.
     \begin{itemize}
+      \item About $2\%$ of the genome.
+      \item Price reduction.
       \item Diagnostics.
     \end{itemize}
   \end{minipage}
 \end{pframe}
 
+\subsection{Clustering}
 \begin{pframe}
   \begin{minipage}[t]{0.47\textwidth}
     \begin{figure}[]
       \begin{center}
         \includegraphics[height=0.88\textheight]{flowcell_2000}
       \end{center}
-      \caption{Flowcell.}
+      \caption{HiSeq flowcell.}
     \end{figure}
   \end{minipage}
   \hfill
@@ -295,6 +284,7 @@
   \end{minipage}
 \end{pframe}
 
+\subsection{Base calling}
 \begin{pframe}
   \begin{figure}[]
     \begin{center}
@@ -304,57 +294,7 @@
   \end{figure}
 \end{pframe}
 
-%\begin{pframe}
-%  \begin{minipage}[t]{0.47\textwidth}
-%    \begin{figure}[]
-%      \begin{center}
-%        \includegraphics[width=0.8\textwidth, height=0.3\textheight]
-%          {k_flowcell}
-%      \end{center}
-%      \caption{Flowcell.}
-%    \end{figure}
-%    \vspace{-1cm}
-%    \begin{figure}[]
-%      \begin{center}
-%        \includegraphics[width=0.8\textwidth]{k_bridge2}
-%      \end{center}
-%      \caption{Amplification.}
-%    \end{figure}
-%  \end{minipage}
-%  \hfill
-%  \pause
-%  \begin{minipage}[t]{0.47\textwidth}
-%  Optical system.
-%  \begin{itemize}
-%    \item DNA fragments are loaded on a flowcell.
-%    \item Fragments are amplified.
-%    \item Clusters of fragments give the same signal.
-%  \end{itemize}
-%  \end{minipage}
-%\end{pframe}
-%
-%\begin{pframe}
-%  \begin{minipage}[t]{0.47\textwidth}
-%    \begin{figure}[]
-%      \begin{center}
-%        \includegraphics[trim=0 0 0 5cm, clip, height=0.9\textheight]{paired_end_2}
-%      \end{center}
-%      \caption{Paired end.}
-%    \end{figure}
-%  \end{minipage}
-%  \hfill
-%  \pause
-%  \begin{minipage}[t]{0.47\textwidth}
-%    Advantages:
-%    \begin{itemize}
-%      \item Mapping to non-unique regions.
-%      \item Structural variation.
-%      \item \textit{De novo} assembly (scaffolding).
-%    \end{itemize}
-%  \end{minipage}
-%\end{pframe}
-%
-\subsection{Life-Tech}
+\subsection{Life-Tech platforms}
 \begin{pframe}
   \begin{minipage}[t]{0.47\textwidth}
     \begin{figure}
@@ -397,6 +337,24 @@
   \end{minipage}
 \end{pframe}
 
+\begin{pframe}
+  These systems use \emph{unlabelled} and \emph{non-blocked} nucleotides.
+  \bigskip
+
+  Unlabelled:
+  \begin{itemize}
+    \item Platform measures pH values.
+    \item Bead amplification to get enough signal.
+  \end{itemize}
+  \bigskip
+
+  Non-blocked:
+  \begin{itemize}
+    \item Only one nucleotide per \emph{flow}.
+    \item Variable read length.
+  \end{itemize}
+\end{pframe}
+
 \begin{pframe}
   \begin{minipage}[t]{0.47\textwidth}
     \begin{figure}[]
@@ -586,7 +544,7 @@
       {per_base_sequence_content}
      \caption{Per base sequence content.}
   \end{figure}
-  \vspace{-0.5cm}
+  \vspace{-0.7cm}
 
   \begin{figure}
     \includegraphics[width=\textwidth, height=0.35\textheight]
@@ -601,7 +559,7 @@
   \begin{minipage}[t]{0.45\textwidth}
     \begin{figure}[]
       \begin{center}
-        \includegraphics[height=0.88\textheight]{k_align}
+        \includegraphics[height=0.8\textheight]{k_align}
       \end{center}
       \caption{Visualisation of an alignment.}
     \end{figure}
@@ -849,128 +807,25 @@
   \end{figure}
 \end{pframe}
 
-%\section{Pipelines}
-%\subsection{Pipelines}
-%\begin{pframe}
-%  \begin{figure}[]
-%    \begin{center}
-%      \includegraphics[height=0.85\textheight]{pipeline}
-%    \end{center}
-%    \caption{A real-life pipeline.}
-%  \end{figure}
-%\end{pframe}
-%
-%\begin{pframe}
-%  \begin{figure}[]
-%    \begin{center}
-%      \includegraphics[height=0.85\textheight]{assemblyline}
-%    \end{center}
-%    \caption{Scene from ``Modern times''.}
-%  \end{figure}
-%\end{pframe}
-%
-%\begin{pframe}
-%  Combining tools:
-%  \begin{itemize}
-%    \item The output of one tool can serve as the input for another.
-%    \item Not necessarily linear.
-%    \item \ldots
-%  \end{itemize}
-%  \bigskip
-%  \pause
-%
-%  Running various different tools:
-%  \begin{itemize}
-%    \item Two or three different aligners.
-%    \item A couple of variant callers.
-%    \item \ldots
-%  \end{itemize}
-%\end{pframe}
-%
-%\subsection{Combining tools}
-%\begin{pframe}
-%  \begin{lstlisting}[language=bash, caption=Shell script]
-%    bwa aln -t 8 $reference $i > $i.sai
-%    bwa samse $reference $i.sai $i > $i.sam
-%    samtools view -bt $reference -o $i.bam $i.sam
-%  \end{lstlisting}
-%  \medskip
-%  \pause
-%
-%  \begin{lstlisting}[language=make, caption=Makefile]
-%    %.sai: %.fq
-%      $(BWA) aln -t $(THREADS) $(call MKREF, $@) $< > $@
-%
-%    %.sam: %.sai %.fq
-%      $(BWA) samse $(call MKREF, $@) $^ > $@
-%
-%    %.bam: %.sam
-%      $(SAMTOOLS) view -bt $(call MKREF, $@) -o $@ $<
-%  \end{lstlisting}
-%\end{pframe}
-%
-%\section{Graphical interfaces}
-%\subsection{Galaxy}
-%\begin{pframe}
-%  Galaxy: a graphical user interface:
-%  \begin{itemize}
-%    \item Wrapper for command line utilities.
-%    \item User friendly.
-%    \item Point and click.
-%    \pause
-%    \item Workflows.
-%    \begin{itemize}
-%      \item Save all the steps you did in your analysis.
-%      \item Rerun the entire analysis on a new dataset.
-%      \item Share your workflow with other people.
-%      \item \ldots
-%    \end{itemize}
-%  \end{itemize}
-%
-%  \vfill
-%  \permfoot{http://galaxy.psu.edu/}
-%\end{pframe}
-%
-%\begin{pframe}
-%  \begin{figure}
-%    \includegraphics[trim=0 0 0 2cm, clip, width=\textwidth]{galaxy}
-%    \caption{Galaxy main user interface}
-%  \end{figure}
-%\end{pframe}
-%
-%\begin{pframe}
-%  \begin{figure}
-%    \includegraphics[width=\textwidth, height=0.9\textheight]{galaxy_mpileup}
-%    \caption{User friendly interface with Galaxy}
-%  \end{figure}
-%\end{pframe}
-%
-%\subsection{Workflow of a parallel pipeline}
-%\begin{pframe}
-%  \begin{figure}
-%    \includegraphics[width=\textwidth, height=0.9\textheight]{gapss3}
-%    \caption{Dependency diagram.}
-%  \end{figure}
-%\end{pframe}
-%
-%\begin{pframe}
-%  \begin{figure}
-%    \includegraphics[trim=320 0 100 70, clip, width=\textwidth,
-%      height=0.9\textheight]{gapss3}
-%    \caption{Zoomed in.}
-%  \end{figure}
-%\end{pframe}
-
 \section{Notes}
 \subsection{Please remember}
 \begin{pframe}
-  We only covered two systems.
+  There are many more NGS systems:
+  \begin{itemize}
+    \item PacBio RSII.
+    \item Roche 454.
+    \item ABI SOLiD.
+  \end{itemize}
   \bigskip
 
-  We only covered a few applications.
+  Other applications:
+  \begin{itemize}
+    \item \emph{De novo} assembly.
+    \item RNA sequencing.
+  \end{itemize}
   \bigskip
 
-  We only gave an outline of the data analysis of this selection.
+  We only gave an outline of the data analysis.
 \end{pframe}
 
 \section{Questions?}