Manuscript Style Guide

Organism Scientific Names

Follow the Wikipedia Manual of Style unless there is a more authoritative source that overrides their guidelines.

LaTeX styling

The point of LaTeX is that you should be encoding the parts of your document based on the semantics. You can fiddle with the formatting later.

To this end, at the top of 0_main.tex, there is a section called Local Definitions that has a set of commands that allow you to mark-up terms and phrases based on what they mean, not based on what you want them to look like. This is important, as it makes it easier to change styles depending on the journals that we need to submit to. It also helps in making sure that we are styling things consistently throughout the document.

Current set of commands

The definitive list is in the LaTeX 0_main.tex file. For convenience, here is a brief listing of commands, and when to use them:

Base commands

• \foreign: Any Latin, neo-Latin (i.e., taxonomic names), or foreign words or phrases ('Coronaviridae', 'ab initio', 'via', 'ergo', etc.)
• \identifier: For accessions, identifiers, etc.
• \program: For proper names of code, algorithms, pipelines, variables, databases, etc.
• \code: For displaying verbatim snippets of code, command-lines, etc.
• \comment: For leaving a in-LaTeX comment.

Serratus-specific commands

To ensure that common terms are styled consistently throughout the document:

• \Serratus
• \SerraTax
• \SerraPlace
• \coronaSPAdes
• \DARTH
• \Tantalus

These are some convenience commands for LaTeX-editing authors to leave one another notes that are tracked via Git:

• \ta: Comment from Tomer
• \ab: Comment from Artem
• \re: Comment from Robert
• \pb: Comment from Pierre
• \ak: Comment from Anton
• \rc: Comment from Rayan

A few common LaTeX style issues to look out for:

• If you find yourself wanting to put in a command to make something bold, underlined, italicized, smaller, larger, etc., you should make a command instead, mark up the text with your new command, and only put formatting in the command definition.
• Want to make a variable name (x) look "mathy"? Use $x$.
• Want to put in a tilde to avoid writing the word "approximately"? Use \textapprox, not a literal ~.
• Want to put in an underscore? Escape it: \_
• Want to write 5' or 3'? Do this: $5\prime$
• Want to emphasize some word as very imporant? Do this: This word is \emph{very} important!
• Putting in a raw URL? Put it inside of a \url command.
• Please put a literal ~ preceding references and citations instead of a single whitespace, so that they don't break across from the word that they are associated with: Figure~\ref{eight}, or amazing results~\cite{BozoTheClown}.