Unix for Bioinformatics
Paragraph(s) of introductory material. Unix is much more than an environment in which you can execute big programmes like bwa or samtools. Rather, with it’s suite of text searching, extraction and manipulation programmes, it is itself a powerful tool for the many small bioinformatic tasks that you will encounter during everyday work.
Before you jump into this tutorial
What learners need to know before tackling this lesson.
This tutorial was first given at a next generation sequencing data analysis workshop in March 2013 at Sheffeld University. This tutorial expects you to do all the steps exactly as written from top to bottom. So refrain from experimenting during the first run through it.
Your command line prompt will end with a $ sign. So a $ sign in this tutorial tells you to type the stuff that comes ‘’’after’’’ the $ sign into your command line. The words “folder” and “directory” mean the same thing. So I use them interchangeably.