Command Line From Zero

A small course designed to introduce you to core aspects of scripting in bioinformatics and genomics.
This module was developed by me for a Physalia Workshop and available here for anyone

Background

Knowing how to work in command line can make troublesome bioinformatic chores a breeze.

However, not everyone has access to an instructor and code is often scattered across dozens of forum pages.

This mini course was designed to consolidate the scattered nuggets of command line prompts into one html markdown.

In the lessons each tab is a seperate topic for you to explore. In the corresponding practice, you will find problem sets and solutions that build on the concepts covered.

Learning these core principle and common commands will provide you with the foundation you need to learn additional topics or solve new informatic challenges, hope you enjoy the course!

Objectives

The objectives of this course are for you to

  • Understand the basics of the command line interface and how it is used in bioinformatics.
  • Learn and apply basic commands to navigate directories, manage files, and move data around
  • Understand how and when to use variables, conditionals, or loops
  • Use grep, sed, and awk to search, manipulate, process or extract data from files
  • Learn and apply ways to automate repetitive tasks
After completion of this course you should be able to apply the knowledge learned to perform basic bioinformatics tasks such as data cleaning and preprocessing, sequence searching and alignment, and data analysis.