\documentclass[10pt,a4paper]{article}

% Packages
\usepackage{fancyhdr}           % For header and footer
\usepackage{multicol}           % Allows multicols in tables
\usepackage{tabularx}           % Intelligent column widths
\usepackage{tabulary}           % Used in header and footer
\usepackage{hhline}             % Border under tables
\usepackage{graphicx}           % For images
\usepackage{xcolor}             % For hex colours
%\usepackage[utf8x]{inputenc}    % For unicode character support
\usepackage[T1]{fontenc}        % Without this we get weird character replacements
\usepackage{colortbl}           % For coloured tables
\usepackage{setspace}           % For line height
\usepackage{lastpage}           % Needed for total page number
\usepackage{seqsplit}           % Splits long words.
%\usepackage{opensans}          % Can't make this work so far. Shame. Would be lovely.
\usepackage[normalem]{ulem}     % For underlining links
% Most of the following are not required for the majority
% of cheat sheets but are needed for some symbol support.
\usepackage{amsmath}            % Symbols
\usepackage{MnSymbol}           % Symbols
\usepackage{wasysym}            % Symbols
%\usepackage[english,german,french,spanish,italian]{babel}              % Languages

% Document Info
\author{ac1513}
\pdfinfo{
  /Title (seqkit.pdf)
  /Creator (Cheatography)
  /Author (ac1513)
  /Subject (seqkit Cheat Sheet)
}

% Lengths and widths
\addtolength{\textwidth}{6cm}
\addtolength{\textheight}{-1cm}
\addtolength{\hoffset}{-3cm}
\addtolength{\voffset}{-2cm}
\setlength{\tabcolsep}{0.2cm} % Space between columns
\setlength{\headsep}{-12pt} % Reduce space between header and content
\setlength{\headheight}{85pt} % If less, LaTeX automatically increases it
\renewcommand{\footrulewidth}{0pt} % Remove footer line
\renewcommand{\headrulewidth}{0pt} % Remove header line
\renewcommand{\seqinsert}{\ifmmode\allowbreak\else\-\fi} % Hyphens in seqsplit
% This two commands together give roughly
% the right line height in the tables
\renewcommand{\arraystretch}{1.3}
\onehalfspacing

% Commands
\newcommand{\SetRowColor}[1]{\noalign{\gdef\RowColorName{#1}}\rowcolor{\RowColorName}} % Shortcut for row colour
\newcommand{\mymulticolumn}[3]{\multicolumn{#1}{>{\columncolor{\RowColorName}}#2}{#3}} % For coloured multi-cols
\newcolumntype{x}[1]{>{\raggedright}p{#1}} % New column types for ragged-right paragraph columns
\newcommand{\tn}{\tabularnewline} % Required as custom column type in use

% Font and Colours
\definecolor{HeadBackground}{HTML}{333333}
\definecolor{FootBackground}{HTML}{666666}
\definecolor{TextColor}{HTML}{333333}
\definecolor{DarkBackground}{HTML}{3711A3}
\definecolor{LightBackground}{HTML}{F2F0F9}
\renewcommand{\familydefault}{\sfdefault}
\color{TextColor}

% Header and Footer
\pagestyle{fancy}
\fancyhead{} % Set header to blank
\fancyfoot{} % Set footer to blank
\fancyhead[L]{
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{C}
    \SetRowColor{DarkBackground}
    \vspace{-7pt}
    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
    }
\end{tabulary}
\columnbreak
\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{seqkit Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{ac1513} via \textcolor{DarkBackground}{\uline{cheatography.com/78065/cs/19074/}}}
\end{tabulary}
\end{multicols}}

\fancyfoot[L]{ \footnotesize
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{LL}
  \SetRowColor{FootBackground}
  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}ac1513 \\
  \uline{cheatography.com/ac1513} \\
  \end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Published 2nd September, 2020.\\
   Updated 22nd March, 2022.\\
   Page {\thepage} of \pageref{LastPage}.
\end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}}  \\
  \SetRowColor{white}
  \vspace{-5pt}
  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
\end{tabulary}
\end{multicols}}




\begin{document}
\raggedright
\raggedcolumns

% Set font size to small. Switch to any value
% from this page to resize cheat sheet text:
% www.emerson.emory.edu/services/latex/latex_169.html
\footnotesize % Small font.

\begin{multicols*}{2}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{grep}}  \tn
% Row 0
\SetRowColor{LightBackground}
-f & pattern file \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
-p & search pattern \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
-v & invert (non-matching) \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
-r & patterns use regular expression \tn 
% Row Count 4 (+ 1)
% Row 4
\SetRowColor{LightBackground}
-n & by name \tn 
% Row Count 5 (+ 1)
% Row 5
\SetRowColor{white}
-s & by seq \tn 
% Row Count 6 (+ 1)
% Row 6
\SetRowColor{LightBackground}
-i & ignore case \tn 
% Row Count 7 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{8.4cm}}{search sequences by pattern(s) of name or sequence motifs}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{fx2tab}}  \tn
% Row 0
\SetRowColor{LightBackground}
-n & print names \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
-i & print id (instead of full header) \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
-g & print gc content \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
-G & print gc-skew \tn 
% Row Count 4 (+ 1)
% Row 4
\SetRowColor{LightBackground}
-l & print length \tn 
% Row Count 5 (+ 1)
% Row 5
\SetRowColor{white}
-B & print base content (e.g. -B AT -B N) \tn 
% Row Count 6 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{sort}}  \tn
% Row 0
\SetRowColor{LightBackground}
-l & by length \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
-n & by full name (not id) \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
-s & by sequence \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
-r & reverse \tn 
% Row Count 4 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{stats}}  \tn
% Row 0
\SetRowColor{LightBackground}
-a & all \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
-T & tabular (machine readable \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
-j & number of threads \tn 
% Row Count 3 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{split}}  \tn
% Row 0
\SetRowColor{LightBackground}
-i & by id \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
-p & into \# parts \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
-s & by size \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
-O & output directory (def. is \$infile.split) \tn 
% Row Count 5 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\SetRowColor{LightBackground}
\mymulticolumn{2}{x{8.4cm}}{use split2 for fastq/paired end (-1 + -2 for paired end)}  \tn 
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{0.8 cm} x{7.2 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{seq}}  \tn
% Row 0
\SetRowColor{LightBackground}
-m & min. length of reads to output e.g. 500 for reads over 500bp \tn 
% Row Count 2 (+ 2)
% Row 1
\SetRowColor{white}
-M & max. length of reads to output e.g. 500 for reads under 500bp \tn 
% Row Count 4 (+ 2)
% Row 2
\SetRowColor{LightBackground}
-n & only print read names \tn 
% Row Count 5 (+ 1)
% Row 3
\SetRowColor{white}
-w & defines line width, 0 for no wrap (i.e. to turn into one-line fastx) \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
-i & print ID instead of full head (shorten ID) \tn 
% Row Count 9 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{p{1.28 cm} x{6.72 cm} }
\SetRowColor{DarkBackground}
\mymulticolumn{2}{x{8.4cm}}{\bf\textcolor{white}{other}}  \tn
% Row 0
\SetRowColor{LightBackground}
faidx & Create fasta index file \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
fq2a & fastq to fasta \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
rmdup & remove duplicated sequences \tn 
% Row Count 3 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}--}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}