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Update chapman_bcbio.tex

added concepts of remaining up to date.
Need a table of sites and architectures upon which the code is actively deployed
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13 papers/bcbio-nextgen/chapman_bcbio.tex
@@ -39,7 +39,7 @@
and cancer tumor/normal pairings. However, rapidly changing best
practice approaches in alignment and variant calling, coupled with
large data sizes, make it a challenge to develop scalable, accurate
-pipelines. Coordinated community development overcomes these
+pipelines that can remain up to date. Coordinated community development overcomes these
challenges by sharing testing and updates across groups relying on the
same infrastructure.
@@ -69,7 +69,7 @@ \section*{Introduction}
mechanism to assess variant quality and interfaces with downstream tools for
variant analysis. Practically, it installs with a single command on multiple
computing architectures, scales to large whole genome analyses, and is community
-developed. The goal is to provide a platform for moving from raw sequencing data
+developed. The goal is to provide a robust platform for moving from raw sequencing data
to high-quality variant calls that evolves as algorithms and sequencing
technologies change.
@@ -116,7 +116,8 @@ \section*{Introduction}
\item Community developed: Due to the focus on solving the problems
of setting up and maintaining a complex analysis pipeline, multiple
- sequencing centers and research laboratories use bcbio-nextgen. We
+ sequencing centers and research laboratories use bcbio-nextgen <<<SUCH AS
+ AND REFER TO A TABLE OF THE SITES AT WHICH IT IS EMPLOYED TOGETEHR WITH THE ARCHITECTURES>>>>. We
actively encourage contributors to the code base and make it easy to
get started with a fully automated installer and updater that
prepares all third party software and reference genomes.
@@ -213,9 +214,9 @@ \section*{Validation}
calling without recalibration and realignment, both HaplotypeCaller and
FreeBayes perform as good or better without these steps.
-The main benefit of validation is to enables experiments that quantitatively
+The main benefit of validation is to enable experiments that quantitatively
assess widely held approaches. We expect best practices to change with new
-releases and algorithms, and the automated assessment mechanism allows
+releases and algorithms. The automated assessment mechanism allows
bcbio-nextgen to track and adapt to continuously improving tools.
\FloatBarrier
@@ -265,7 +266,7 @@ \section*{Scaling}
memory usage and disk IO to maximize the throughput of multiple simultaneous
processes. An input configuration files specifies available memory usage for
programs that allow memory restrictions, and expected memory usage for those
-that do not. These inputs allow an accurate estimate of memory consumption and
+that do not. These inputs allow for an accurate estimate of memory consumption and
bcbio-nextgen avoids overscheduling jobs relative to available memory on each
machine. Similarly, simultaneous disk IO on shared filesystems is a common
bottleneck during processing. bcbio-nextgen minimizes this by use of streaming

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