Commit d49f2af0 authored by Laros's avatar Laros
Browse files

Updated some typos and statistics.

parent c472296b
......@@ -109,7 +109,7 @@
\end{pframe}
\begin{pframe}
Standard score ($z$-score):
Standard score ($z$-score) of a raw score $x$:
\begin{displaymath}
z = \frac{x - \mu}{\sigma}
\end{displaymath}
......@@ -184,19 +184,24 @@
\begin{pframe}
The pipeline is straightforward:
\begin{itemize}
\item Alignment to the reference genomen (GRCh37, hg19).
\item Alignment to the reference genome (GRCh37, hg19).
\item Deduplication.
\item CNV calling.
\end{itemize}
\bigskip
Original run time: $5$ to $6$ hours.
Original run time: $6$ hours, but with up to $500$ samples per week.
\begin{itemize}
\item $20$ minutes per sample.
\end{itemize}
\bigskip
\pause
We expect up to $500$ samples per week.
Additional constraint: $8$ (office) hours turnaround time.
\begin{itemize}
\item $20$ minutes per sample.
\item No room for delays.
\item $2.5$ minutes per sample ($2$ batches of $96$ samples).
\pause
\item Implementation time of two months.
\end{itemize}
\end{pframe}
......@@ -207,8 +212,11 @@
\item Other aligner (\lstinline{BWA mem}).
\item Other computational framework (\lstinline{Snakemake}).
\end{itemize}
\bigskip
These improvements brought the runtime back to around $40$ minutes per sample.
\bigskip
\pause
Parallel processing on the LUMC cluster.
\begin{itemize}
......@@ -216,6 +224,8 @@
\item Between $90$ and $180$ minutes per batch.
\begin{itemize}
\item Depending on the number of batches per flowcell.
\pause
\item Around $56$ seconds per sample.
\end{itemize}
\end{itemize}
\end{pframe}
......@@ -256,13 +266,6 @@
\item Florea: API adapter for the HPC cluster.
\item Amegilla: API adapter for legacy / proprietary systems.
\end{itemize}
%\bigskip
%Common framework:
%\begin{itemize}
% \item Nginx, REST.
% \item X.509 certificates.
%\end{itemize}
\vfill
\permfoot{\url{https://git.lumc.nl/groups/apis}}
......@@ -324,6 +327,10 @@
\item Monitor the pipeline progress.
\item Keep track of the status (query via the API).
\end{itemize}
\bigskip
Once the pipeline is finished, a status update is reported back to the
submitter of the pipeline run.
\end{pframe}
\subsection{Underlying infrastructure}
......
Subproject commit e8f15b637cab7194573357c7a09b0efb709c7c1c
Subproject commit 49bd4b899df12078e4c9e93e766960bb0d5bf951
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