Scientific Computing
Shell scripting
Network
High-performance computing
Conda/virtual environments
Nextflow
References
Unix general
A Book for Anyone to Get Started with Unix. http://seankross.com/the-unix-workbench/, and the GitHub repository, https://github.com/seankross/the-unix-workbench
Data Coding 101 – Intro To Bash. Four episodes, video. https://data36.com/data-coding-bash-best-practices/
An interactive explainer of any shell command. http://explainshell.com/
Unix/Linux command reference sheets. https://cheat-sheets.s3.amazonaws.com/linux-commands-cheat-sheet-new.pdf and https://files.fosswire.com/2007/08/fwunixref.pdf
Survival guide for Unix newbies. http://matt.might.net/articles/basic-unix/
Settling into Unix tutorial. http://matt.might.net/articles/settling-into-unix/
Shell programming with bash tutorial. http://matt.might.net/articles/bash-by-example/
Master the power of command-line with a list of one-liner gems. http://www.commandlinefu.com/commands/browse
“The Unix shell”, Software Carpentry. https://swcarpentry.github.io/shell-novice/
A curated list of Terminal frameworks, plugins & resources for command-line interface (CLI) lovers. http://terminalsare.sexy and https://github.com/k4m4/terminals-are-sexy
“Data Science at the Command Line” by Jeroen Janssens, GitHub repository https://github.com/jeroenjanssens/data-science-at-the-command-line and an online book https://www.datascienceatthecommandline.com/
Unix in Bioinformatics
Heng Li’s “A Bioinformatician’s UNIX Toolbox”, http://lh3lh3.users.sourceforge.net/biounix.shtml
Bioinformatics one-liners by Stephen Turner, https://github.com/stephenturner/oneliners
Collection of bioinformatics-genomics bash one liners, using awk, sed etc. https://github.com/crazyhottommy/bioinformatics-one-liners
Links and references to many genomics and bioinformatics resources, https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources
Text manipulation in Unix
Regular expression, Unix commands, Python quick reference, SQL reference card. PCfB_Appendices.pdf
Tutorial to
sedby Bruce Barnett. http://www.grymoire.com/Unix/Sed.htmlInteractive Vim tutorial. http://www.openvim.com/
Vim reference card. http://web.mit.edu/merolish/Public/vi-ref.pdf