6.3
The Command Line Tool
NGS analyses are performed in most cases using the terminal (Fig. 6.2). The command line
interpreter Bash will translate and execute commands entered after the prompt ($). A basic
overview of essential Unix/Linux commands that will allow you to navigate a file system
and move, copy, edit files is provided in the Command line Bootcamp (http://korflab.
ucdavis.edu/bootcamp.html) by Keith Bradnam. A beginner level Linux/Unix expertise is
sufficient to get started and to perform the majority of analyses that we cover in this book.
The basic Linux/Unix commands, their meaning and description are depicted in
Table 6.1. Each command is composed of three parts:
• The command.
• Options/ flags.
• Arguments.
/
usr
bin
dev
etc
sbin
home
usr
var
tmp
opt
Fig. 6.1 Linux/Unix file system
Fig. 6.2 The terminal using the CLI Bash
6 Introduction to Command Line (Linux/Unix)
73