Merge pull request #179 from percyfal/author-update

Add PU author affiliations and acknowledgements

paper.tex

@@ -48,6 +48,7 @@
 \author[8]{Sam Tallman} % https://orcid.org/0000-0001-7183-6276
 \author[1]{Rafal Wojdyla} % https://orcid.org/0009-0005-0735-7090
 \author[9]{Shadi Zabad} % https://orcid.org/0000-0002-8003-9284
+\author[10]{Per Unneberg} % https://orcid.org/0000-0001-5735-3315
 
 % Senior 
 \author[1,\authfn{2}]{Jeff Hammerbacher} % https://orcid.org/0000-0001-6596-8563
@@ -64,6 +65,9 @@
 \affil[7]{Wellcome Sanger Institute}
 \affil[8]{Genomics England}
 \affil[9]{School of Computer Science, McGill University, Montreal, QC, Canada}
+\affil[10]{Department of Cell and Molecular Biology, National
+  Bioinformatics Infrastructure Sweden, Science for Life Laboratory,
+  Uppsala University, Uppsala, Sweden}
 
 %%% Author Notes
 \authnote{\authfn{1}Joint first author.}
@@ -1022,33 +1026,34 @@ \subsection{Case study: 1,063 spruce whole-genome samples}
 \toprule
 {Field} & {type} & {storage} & {compress} & {\%total} \\
   \midrule
-  /call\_PL & int16 & 6.12 TiB & 12.0 & 92.75\% \\
-  /call\_genotype & int8 & 282.45 GiB & 26.0 & 4.18\% \\
-  /call\_genotype\_mask & bool & 42.15 GiB & 180.0 & 0.62\% \\
-  /variant\_DP4 & int32 & 26.24 GiB & 2.1 & 0.39\% \\
-  /variant\_MQSBZ & float32 & 13.08 GiB & 1.1 & 0.19\% \\
-  /variant\_RPBZ & float32 & 13.04 GiB & 1.1 & 0.19\% \\
-  /variant\_MQBZ & float32 & 12.97 GiB & 1.1 & 0.19\% \\
-  /variant\_SCBZ & float32 & 12.94 GiB & 1.1 & 0.19\% \\
-  /variant\_VDB & float32 & 12.84 GiB & 1.1 & 0.19\% \\
-  /variant\_quality & float32 & 12.84 GiB & 1.1 & 0.19\% \\
-  /variant\_BQBZ & float32 & 12.64 GiB & 1.1 & 0.19\% \\
-  /variant\_SGB & float32 & 12.12 GiB & 1.2 & 0.18\% \\
-  /variant\_position & int32 & 9.65 GiB & 1.4 & 0.14\% \\
-  /variant\_AC & int16 & 7.42 GiB & 2.8 & 0.11\% \\
-  /variant\_DP & int32 & 6.71 GiB & 2.1 & 0.10\% \\
-  /variant\_allele & object & 5.37 GiB & 21.0 & 0.08\% \\
-  /variant\_AN & int16 & 3.05 GiB & 2.3 & 0.05\% \\
-  /call\_genotype\_phased & bool & 2.03 GiB & 1800.0 & 0.03\% \\
-  /variant\_filter & bool & 1.46 GiB & 2.4 & 0.02\% \\
-  /variant\_MQ & int8 & 489.83 MiB & 7.3 & 0.01\% \\
+  /call\_PL & int16 & 6.1 TiB & 12.0 & 92.75\% \\
+  /call\_genotype & int8 & 282.5 GiB & 26.0 & 4.18\% \\
+  /call\_genotype\_mask & bool & 42.2 GiB & 180.0 & 0.62\% \\
+  /variant\_DP4 & int32 & 26.2 GiB & 2.1 & 0.39\% \\
+  /variant\_MQSBZ & float32 & 13.1 GiB & 1.1 & 0.19\% \\
+  /variant\_RPBZ & float32 & 13.0 GiB & 1.1 & 0.19\% \\
+  /variant\_MQBZ & float32 & 13.0 GiB & 1.1 & 0.19\% \\
+  /variant\_SCBZ & float32 & 12.9 GiB & 1.1 & 0.19\% \\
+  /variant\_VDB & float32 & 12.8 GiB & 1.1 & 0.19\% \\
+  /variant\_quality & float32 & 12.8 GiB & 1.1 & 0.19\% \\
+  /variant\_BQBZ & float32 & 12.6 GiB & 1.1 & 0.19\% \\
+  /variant\_SGB & float32 & 12.1 GiB & 1.2 & 0.18\% \\
+  /variant\_position & int32 & 9.7 GiB & 1.4 & 0.14\% \\
+  /variant\_AC & int16 & 7.4 GiB & 2.8 & 0.11\% \\
+  /variant\_DP & int32 & 6.7 GiB & 2.1 & 0.10\% \\
+  /variant\_allele & object & 5.4 GiB & 21.0 & 0.08\% \\
+  /variant\_AN & int16 & 3.1 GiB & 2.3 & 0.05\% \\
+  /call\_genotype\_phased & bool & 2.0 GiB & 1800.0 & 0.03\% \\
+  /variant\_filter & bool & 1.5 GiB & 2.4 & 0.02\% \\
+  /variant\_MQ & int8 & 489.8 MiB & 7.3 & 0.01\% \\
   \bottomrule
 \end{tabular}
 \end{table}
 
 Table~\ref{tab-spruce-data} shows that the dataset storage size is
 dominated by a major component, call\_PL, which accounts for nearly
-93\% of the total. call\_PL is yet another field with low compression potential due to inherent noisiness.
+93\% of the total. call\_PL is yet another field with low compression
+potential due to inherent noisiness.
 
 %% FIXME: reference regarding VCF POS?
 The spruce data set poses an interesting challenge to the VCF storage
@@ -1644,7 +1649,10 @@ \subsection{Funding}
 JK and AM acknowledge the Bill \& Melinda Gates Foundation (INV-001927).
 TM acknowledges funding from The New Zealand Institute for Plant \& Food
 Research Ltd Kiwifruit Royalty Investment Programme.
-
+PU was supported by the SciLifeLab \& Wallenberg Data Driven Life
+Science Program, Knut and Alice Wallenberg Foundation (grants: KAW
+2020.0239 and KAW 2017.0003), and by the National Bioinformatics
+Infrastructure Sweden (NBIS) at SciLifeLab
 % \subsection{Author's Contributions}
 
 \section{Acknowledgements}
@@ -1665,6 +1673,11 @@ \section{Acknowledgements}
 Biomedical Research Centre. The views expressed are those of the author(s) and
 not necessarily those of the NHS, the NIHR or the Department of Health.
 
+Computation for the Spruce case study were enabled by resources
+provided by the National Academic Infrastructure for Supercomputing in
+Sweden (NAISS), partially funded by the Swedish Research Council
+through grant agreement no. 2022-06725.
+
 Genozip was used under the terms of the free Genozip Academic license.
 Genozip was only used on simulated data, in compliance with
 the ``No Commercial Data'' criterion.