Other Programming Languages Common in Bioinformatics

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Shell scripting

During the course of your work you may need to do a simple task on a large number of files, like renaming all the files from a sequencing run, or raising the contrast on microscopy images. Performing these tasks on individual files by hand is time-consuming and prone to errors. Unix, Mac OSX and Windows all have simple shell scripting programming languages built-in for these small repetitive tasks require simple logic

The benefits of shell scripting are:

  1. not needing to install additional software on your computer and,
  2. ease of use. Most Unix-based systems (eg. Ubuntu) come with the Bourn Again SHell (“Bash”), which are also standard on Mac OSX systems. Windows have the Command Prompt and PowerShell. You can enter shell scripting commands directly via a command line interface or save these commands in a shell script to be run immediately non-interactively.

Shell scripting resources


The Julia language aims to combine the accessible syntax of R or Python with the speed of C/C++ programs. While not currently as functional as R or Python for bioinformatic tasks, there is a growing collection of resources for Julia for bioinformatics.


Go, or GoLang also has some support for data science.


Perl is a computational language often found in bioinformatic analyses. The language was originally developed in 1987. perl.org has numerous tutorials and modules for learning the language.

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