Commit d49f2af0 authored by Laros's avatar Laros
Browse files

Updated some typos and statistics.

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