impg-paper/main.tex at main · pangenome/impg-paper · GitHub

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[noinfo]{bioinfo}
\copyrightyear{2026}
\pubyear{2026}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx}
\usepackage{verbatim}

\usepackage[]{multibib}
\newcites{Meth}{Methods References}

\usepackage{paralist}
\usepackage{lineno}
%\linenumbers

\usepackage{siunitx}
\usepackage{booktabs}
\usepackage{xcolor}
\usepackage{float}
\usepackage{hyperref}

\raggedbottom

\access{Advance Access Publication Date: Day Month Year}
\appnotes{Original Paper}

\begin{document}
\firstpage{1}
\subtitle{Genome analysis}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title[IMPG]{Implicit pangenome graphs}
\author[]{
Andrea Guarracino\,$^{\text{\sfb 1,2},*}$,
Bryce Kille\,$^{\text{\sfb 3}}$,
\ldots,
Erik Garrison\,$^{\text{\sfb 1},*}$
}
\address{
$^{\text{\sf 1}}$Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA \\
$^{\text{\sf 2}}$Bioinnovation and Genome Sciences, The Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA \\
$^{\text{\sf 3}}$Illumina Inc., San Diego, CA 92122, USA
}
\corresp{$^\ast$To whom correspondence should be addressed.}
\history{}
\editor{}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\abstract{
Querying genomic relationships across hundreds of genomes currently requires either constructing computationally expensive graph structures or using projection tools limited to pairwise mappings between individual genomes. Here we introduce implicit pangenome graphs, a framework that treats pairwise alignments as a queryable pangenome representation, making population-scale analysis accessible on commodity hardware without upfront graph construction.
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\maketitle

%\keywords{pangenomes, pangenome graphs, genome alignment, transitive queries, coordinate projection, population genomics}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Sections
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{sections/01.introduction}
\input{sections/02.methods-overview}
\input{sections/03.results}
\input{sections/04.discussion}
\input{sections/05.acknowledgments}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\clearpage
\bibliographystyle{natbib}
\bibliography{bibliography}

\clearpage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Figures
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{sections/06.figures}

\clearpage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Detailed Methods
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{sections/07.methods-detail}

\bibliographystyleMeth{natbib}
\bibliographyMeth{bibliographyMeth}

\clearpage

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Supplementary
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{sections/08.supplementary}

\end{document}