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manuscript.tex
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is just an example/guide for you to refer to when submitting manuscripts to Frontiers, it is not mandatory to use Frontiers .cls files nor frontiers.tex %
% This will only generate the Manuscript, the final article will be typeset by Frontiers after acceptance.
% %
% %
% When submitting your files, remember to upload this *tex file, the pdf generated with it, the *bib file (if bibliography is not within the *tex) and all the figures.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Version 3.4 Generated 2022/06/14 %%%
%%% You will need to have the following packages installed: datetime, fmtcount, etoolbox, fcprefix, which are normally inlcuded in WinEdt. %%%
%%% In http://www.ctan.org/ you can find the packages and how to install them, if necessary. %%%
%%% NB logo1.jpg is required in the path in order to correctly compile front page header %%%
\documentclass[utf8]{FrontiersinHarvard} % for articles in journals using the Harvard Referencing Style (Author-Date), for Frontiers Reference Styles by Journal: https://zendesk.frontiersin.org/hc/en-us/articles/360017860337-Frontiers-Reference-Styles-by-Journal
%\documentclass[utf8]{FrontiersinVancouver} % for articles in journals using the Vancouver Reference Style (Numbered), for Frontiers Reference Styles by Journal: https://zendesk.frontiersin.org/hc/en-us/articles/360017860337-Frontiers-Reference-Styles-by-Journal
%\documentclass[utf8]{frontiersinFPHY_FAMS} % Vancouver Reference Style (Numbered) for articles in the journals "Frontiers in Physics" and "Frontiers in Applied Mathematics and Statistics"
%\setcitestyle{square} % for articles in the journals "Frontiers in Physics" and "Frontiers in Applied Mathematics and Statistics"
\usepackage{url,hyperref,lineno,microtype,subcaption}
\usepackage[onehalfspacing]{setspace}
\linenumbers
% Leave a blank line between paragraphs instead of using \\
\input{manuscript/authors.tex}
\begin{document}
\onecolumn
\firstpage{1}
\title[Pathogen Pangenome Graphs]{Pangenome Graphs in Infectious Disease: A Promising and Practical Implementation for Comprehensive Genetic Variation Analysis}
\author[\firstAuthorLast ]{\Authors} %This field will be automatically populated
\address{} %This field will be automatically populated
\correspondance{} %This field will be automatically populated
\extraAuth{}% If there are more than 1 corresponding author, comment this line and uncomment the next one.
%\extraAuth{corresponding Author2 \\ Laboratory X2, Institute X2, Department X2, Organization X2, Street X2, City X2 , State XX2 (only USA, Canada and Australia), Zip Code2, X2 Country X2, email2@uni2.edu}
\maketitle
\input{manuscript/abstract.tex}
\section{Introduction}
\input{manuscript/intro.tex}
\section{Materials & Methods}
\input{manuscript/mandm.tex}
\section{Results}
\input{manuscript/results.tex}
\section{Discussion}
\section{Nomenclature}
\subsection{Figures}
Frontiers requires figures to be submitted individually, in the same order as they are referred to in the manuscript. Figures will then be automatically embedded at the bottom of the submitted manuscript. Kindly ensure that each table and figure is mentioned in the text and in numerical order. Figures must be of sufficient resolution for publication \href{https://www.frontiersin.org/about/author-guidelines#ImageSizeRequirements}{see here for examples and minimum requirements}. Figures which are not according to the guidelines will cause substantial delay during the production process. Please see \href{https://www.frontiersin.org/about/author-guidelines#FigureRequirementsStyleGuidelines}{here} for full figure guidelines. Cite figures with subfigures as figure \ref{fig:Subfigure 1} and \ref{fig:Subfigure 2}.
\subsection{Tables}
Tables should be inserted at the end of the manuscript. Please build your table directly in LaTeX.Tables provided as jpeg/tiff files will not be accepted. Please note that very large tables (covering several pages) cannot be included in the final PDF for reasons of space. These tables will be published as \href{http://home.frontiersin.org/about/author-guidelines#SupplementaryMaterial}{Supplementary Material} on the online article page at the time of acceptance. The author will be notified during the typesetting of the final article if this is the case.
\section*{Conflict of Interest Statement}
%All financial, commercial or other relationships that might be perceived by the academic community as representing a potential conflict of interest must be disclosed. If no such relationship exists, authors will be asked to confirm the following statement:
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
\section*{Author Contributions}
The Author Contributions section is mandatory for all articles, including articles by sole authors. If an appropriate statement is not provided on submission, a standard one will be inserted during the production process. The Author Contributions statement must describe the contributions of individual authors referred to by their initials and, in doing so, all authors agree to be accountable for the content of the work. Please see \href{https://www.frontiersin.org/about/policies-and-publication-ethics#AuthorshipAuthorResponsibilities}{here} for full authorship criteria.
\section*{Funding}
Details of all funding sources should be provided, including grant numbers if applicable. Please ensure to add all necessary funding information, as after publication this is no longer possible.
\section*{Acknowledgments}
This is a short text to acknowledge the contributions of specific colleagues, institutions, or agencies that aided the efforts of the authors.
\section*{Supplemental Data}
\href{http://home.frontiersin.org/about/author-guidelines#SupplementaryMaterial}{Supplementary Material} should be uploaded separately on submission, if there are Supplementary Figures, please include the caption in the same file as the figure. LaTeX Supplementary Material templates can be found in the Frontiers LaTeX folder.
\section*{Data Availability Statement}
The datasets [GENERATED/ANALYZED] for this study can be found in the [NAME OF REPOSITORY] [LINK].
% Please see the availability of data guidelines for more information, at https://www.frontiersin.org/about/author-guidelines#AvailabilityofData
\bibliographystyle{Frontiers-Harvard} % Many Frontiers journals use the Harvard referencing system (Author-date), to find the style and resources for the journal you are submitting to: https://zendesk.frontiersin.org/hc/en-us/articles/360017860337-Frontiers-Reference-Styles-by-Journal. For Humanities and Social Sciences articles please include page numbers in the in-text citations
%\bibliographystyle{Frontiers-Vancouver} % Many Frontiers journals use the numbered referencing system, to find the style and resources for the journal you are submitting to: https://zendesk.frontiersin.org/hc/en-us/articles/360017860337-Frontiers-Reference-Styles-by-Journal
\bibliography{test}
%%% Make sure to upload the bib file along with the tex file and PDF
%%% Please see the test.bib file for some examples of references
\section*{Figure captions}
%%% Please be aware that for original research articles we only permit a combined number of 15 figures and tables, one figure with multiple subfigures will count as only one figure.
%%% Use this if adding the figures directly in the mansucript, if so, please remember to also upload the files when submitting your article
%%% There is no need for adding the file termination, as long as you indicate where the file is saved. In the examples below the files (logo1.eps and logos.eps) are in the Frontiers LaTeX folder
%%% If using *.tif files convert them to .jpg or .png
%%% NB logo1.eps is required in the path in order to correctly compile front page header %%%
\begin{figure}[h!]
\begin{center}
\includegraphics[width=10cm]{logo1}% This is a *.eps file
\end{center}
\caption{ Enter the caption for your figure here. Repeat as necessary for each of your figures}\label{fig:1}
\end{figure}
\setcounter{figure}{2}
\setcounter{subfigure}{0}
\begin{subfigure}
\setcounter{figure}{2}
\setcounter{subfigure}{0}
\centering
\begin{minipage}[b]{0.5\textwidth}
\includegraphics[width=\linewidth]{logo1.eps}
\caption{This is Subfigure 1.}
\label{fig:Subfigure 1}
\end{minipage}
\setcounter{figure}{2}
\setcounter{subfigure}{1}
\begin{minipage}[b]{0.5\textwidth}
\includegraphics[width=\linewidth]{logo2.eps}
\caption{This is Subfigure 2.}
\label{fig:Subfigure 2}
\end{minipage}
\setcounter{figure}{2}
\setcounter{subfigure}{-1}
\caption{Enter the caption for your subfigure here. \textbf{(A)} This is the caption for Subfigure 1. \textbf{(B)} This is the caption for Subfigure 2.}
\label{fig: subfigures}
\end{subfigure}
%%% If you don't add the figures in the LaTeX files, please upload them when submitting the article.
%%% Frontiers will add the figures at the end of the provisional pdf automatically
%%% The use of LaTeX coding to draw Diagrams/Figures/Structures should be avoided. They should be external callouts including graphics.
\end{document}