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Laros
lectures
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d49f2af0
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d49f2af0
authored
Jun 19, 2017
by
Laros
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Updated some typos and statistics.
parent
c472296b
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lectures/nipt_dataanalysis/nipt_dataanalysis.tex
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...
...
@@ -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 genome
n
(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
}
...
...
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