Updated and moved cover letter.

coverletter/coverletter.md

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+---
+size: 11pt
+draft: no
+sig:
+ include: yes
+ sign: yes
+ post: Associate Professor
+cc:
+---
+
+\today
+
+To the editors of mSystems:
+
+We submit for your review: "Biogeography and Environmental Conditions Shape Phage and Bacteria Interaction Networks Across the Healthy Human Microbiome" by Geoffrey Hannigan and colleagues. We believe this work to be especially well suited for publication in mSystems and highly relevant to a broader scientific readership as well as the general public.
+
+Previous work has focused on studying the human microbiome bacterial and viral communities separately, relying on metrics such as community composition and diversity. These metrics fail to account for the relationships between bacteria and viruses, which account for much of the behavior of these two communities. To address this knowledge and methodological gap, we performed a re-analysis of three existing bacterial and viral metagenomic datasets using network-based techniques that allowed us to focus on the relationships between these interacting communities. Our findings provide new insight into the ecological networks of human bacterial and viral communities. The methods we implemented also provide an additional avenue for future microbiome researchers to build off of.
+
+Our lab strives to set high standards of reproducibility and transparency, while generating and publishing high quality data. As such, all analysis work-flows, scripts, and datasets have been made publicly available for other researchers to utilize.
+
+The data presented in this manuscript are original and the manuscript is not under consideration elsewhere. A preprint version of this manuscript has been made available through BioRxiv (doi: PENDING). All authors have read and approve the manuscript for publication.
+
+We suggest Katrine Whiteson and Anthony Fodor as appropriate handling editors.
+
+We suggest the following reviewers for this publication:
+
+| **Bonnie Hurwitz, PhD**
+| Assistant Professor
+| Dept. of Agricultural and BioSystems Engineering
+| University of Arizona
+| Email: bhurwitz@email.arizona.edu
+
+| **David Pride, MD**
+| Assistant Professor
+| Dept. of Pathology
+| University of California San Diego
+| Email: dpride@ucsd.edu
+
+\newpage
+
+| **K. Eric Wommack, PhD**
+| Professor
+| Dept. of Plant and Soil Sciences
+| Dept. of Marine Biology and Biochemistry
+| University of Delaware
+| Email: wommack@dbi.udel.edu
+
+Unfortunately, we must ask that Rob Knight and Matthew Sullivan not be used as an editor or reviewers since previous interactions with these individuals indicate that they are unable to provide an unbiased assessment of our work.
+
+We thank you for your consideration and look forward to your response.

coverletter/customtemplate.tex

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+%!TEX program = xelatex 
+
+\documentclass[$size$]{letter}
+\usepackage[letterpaper,margin=1in]{geometry}
+
+\usepackage{fixltx2e}
+
+% Adds microtypography features: character protrusion, for XeTeX.
+\usepackage{microtype}
+
+% Allows links.
+\usepackage[usenames,dvipsnames]{color}
+\usepackage[xetex, bookmarks, colorlinks, breaklinks]{hyperref}
+\hypersetup{colorlinks=true, urlcolor=NavyBlue, linkcolor=NavyBlue}
+
+\urlstyle{rm}
+
+\frenchspacing{}        % Remove extra spaces after periods.
+\pagestyle{empty}       % Remove page numbers.
+
+\usepackage{fontspec}
+\defaultfontfeatures{Mapping=tex-text}  % Sets quotation marks.
+\setromanfont{Times}
+\setsansfont[BoldFont={Helvetica Neue Bold}]{Helvetica Neue}
+\setmonofont[Scale=MatchLowercase]{Helvetica}
+
+% From default template
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+\newcommand\shyp{\-}
+
+\newcommand{\header}[0]{
+    {\hypersetup{hidelinks}
+    \noindent
+    \parbox[b][0.625in][t]{6.5in}{
+        \vspace{-0.375in}
+        \parbox[b][0.625in][t]{3.74in}
+            {\href{http://www.umich.edu}
+            {\includegraphics[height=1in]{./Michigan.pdf}}}\hfill
+        \parbox[b][0.625in][t]{2in}{
+            \setlength{\baselineskip}{9pt}
+            \fontsize{7pt}{7pt}{
+                \fontspec{Helvetica}
+                \href{http://www.schlosslab.org}{\textbf{PATRICK D SCHLOSS, PHD}}\\
+                \href{https://medicine.umich.edu/dept/microbiology-immunology/}{Department of Microbiology %
+                    \& Immunology}\vspace{6pt}\\
+                1150 W MEDICAL CENTER DR. 1526 MSRB I\\
+                ANN ARBOR, MICHIGAN 48109-0620\\
+                Phone: (734) 647-5801\\
+                Fax: (734) 764-3562\\
+                \href{mailto:pschloss@umich.edu}{pschloss@umich.edu}
+                }
+            }
+        }}
+    }
+
+$if(draft)$
+\usepackage{draftwatermark}
+\SetWatermarkLightness{0.9}
+$endif$
+
+\begin{document}
+
+\header
+
+\vspace{0.5in}
+
+$body$
+
+$if(sig.include)$
+    \begin{minipage}[t]{6.5in}
+    Sincerely,\\
+
+    \vspace{0.5in}
+
+    $if(sig.sign)$
+        \vspace{-0.2in}\includegraphics[height=0.5in]{./Signature.pdf}
+    $else$
+        \\
+    $endif$
+    \\
+    Patrick D. Schloss\\
+    $sig.post$
+    \end{minipage}
+$endif$
+
+$if(cc)$
+    cc: $for(cc)$$cc$$sep$, $endfor$
+$endif$
+
+$if(ps)$
+    $ps$
+$endif$
+
+\end{document}

coverletter/missfont.log

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+mktextfm arial
+mktextfm arial
+mktextfm arial
+mktextfm Inconsolata
+mktextfm Inconsolata
+mktextfm Inconsolata
+mktextfm Inconsolata
+mktextfm Inconsolata
+mktextfm Inconsolata

coverletter/options.sty

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+\usepackage{setspace}
+\doublespacing
+\usepackage[vmargin=1in,hmargin=1in]{geometry}
+\usepackage{lineno}
+\linenumbers
+\usepackage{parskip}
+\setlength{\parskip}{7.5pt}
+\exhyphenpenalty=10000
+\hyphenpenalty=10000
+
+\newcommand{\beginsupplement}{%
+        \setcounter{table}{0}
+        \renewcommand{\thetable}{S\arabic{table}}%
+        \setcounter{figure}{0}
+        \renewcommand{\thefigure}{S\arabic{figure}}%
+     }

coverletter/renderletter

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+#! /bin/bash
+
+echo Running Pandoc...
+pandoc --latex-engine=xelatex --template=customtemplate.tex -s ./coverletter.md -f markdown -t latex -o ./coverletter.pdf
+echo Done

coverletter/rendermanuscript

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+#! /bin/bash
+
+echo Running Pandoc...
+pandoc --latex-engine=xelatex --template=customtemplate.tex -s ./coverletter.md -f markdown -t latex -o ./coverletter.pdf
+echo Done