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% Metadata Information
\jname{Xxxx. Xxx. Xxx. Xxx.}
\jvol{AA}
\jyear{YYYY}
\doi{10.1146/((please add article doi))}


% Document starts
\begin{document}

\newcommand{\shorttitle}{Pangenome graphs}
\newcommand{\firstauthorlastname}{Eizenga}

% Page header
\markboth{\firstauthorlastname\ et al.}{\shorttitle}

% Title
\title{\shorttitle}


%Authors, affiliations address.
\author{%
  Jordan M \firstauthorlastname$^1$\orcidicon{0000-0001-8345-8356},
  Adam M Novak$^1$\orcidicon{0000-0001-5828-047X},
  \\
  Jonas A Sibbesen$^1$\orcidicon{0000-0002-5528-0236},
  Simon Heumos$^2$\orcidicon{0000-0003-3326-817X},
  \\
  Ali Ghaffaari$^{5,6,7}$,
  Glenn Hickey$^1$,
  Xian Chang$^1$,
  \\
  Josiah D Seaman$^{3,4}$\orcidicon{0000-0003-2374-630X},
  Robin Rounthwaite$^1$\orcidicon{0000-0002-0264-7487},
  Jana Ebler$^{5,6,7}$,
  Mikko Rautiainen$^{5,6,7}$\orcidicon{0000-0003-2971-267X},
  \\
  Shilpa Garg$^{8,9,10}$,
  Benedict Paten$^1$\orcidicon{0000-0001-8863-3539},
  \\
  Tobias Marschall$^{5,6}$\orcidicon{0000-0002-9376-1030},
  Jouni Sir\'{e}n$^1$\orcidicon{0000-0001-5828-4139},
  \\
  and Erik Garrison$^{*1}$\orcidicon{0000-0003-3821-631X}
\affil{\tiny$^1$Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA, 95064}
\affil{\tiny$^2$Quantitative Biology Center, University of Tübingen, Tübingen, Germany, 72076}
\affil{\tiny$^3$Royal Botanic Gardens Kew, Richmond, UK, TW9 3AB}
\affil{\tiny$^4$Queen Mary University of London, London, UK, E1 4NS}
\affil{\tiny$^5$Center for Bioinformatics, Saarland University, Saarbr\"{u}cken, Germany, 66123}
\affil{\tiny$^6$Max Planck Institute for Informatics, Saarbr\"{u}cken, Germany, 66123}
\affil{\tiny$^7$Saarbr\"{u}cken Graduate School for Computer Science, Saarbr\"{u}cken, Germany, 66123}
\affil{\tiny$^8$Department of Genetics, Harvard Medical School, Boston, MA 02215}
\affil{\tiny$^9$Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215}
\affil{\tiny$^{10}$Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215}
\affil{\tiny$\sigma$ORCID identifier hyperlinks}
\affil{\tiny$^*$corresponding author: erik.garrison@ucsc.edu}
}

%Abstract
\begin{abstract}
  Low-cost whole genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms.
  In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes.
  These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies.
  The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping.
  Pangenome graphs stand to become a ubiquitous tool in genomics.
  Although it is unclear if they will replace linear reference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.
\end{abstract}

%Keywords, etc.
\begin{keywords}
  pangenome, genome graph, variation graph
\end{keywords}
\maketitle

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\input{sections/intro}
\input{sections/models}
\input{sections/relating}
\input{sections/formats}
\input{sections/applications}
\input{sections/discussion}
\input{sections/endmatter}
\input{sections/figures}
\input{sections/tables}

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\end{document}