Introduction to the Command Line for Metagenomics

Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

There are quite a few reasons to start learning about the shell:

For most bioinformatics tools, you have to use the shell. There is no graphical interface. If you want to work in metagenomics or genomics you’re going to need to use the shell.
The shell gives you power. The command line gives you the power to do your work more efficiently and more quickly. When you need to do things tens to hundreds of times, knowing how to use the shell is transformative.
To use remote computers or cloud computing, you need to use the shell.

Getting Started

This lesson assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including how a DNA sequence looks like. Participants should bring their laptops and plan to participate actively.

This lesson is part of a workshop that uses data hosted on an Amazon Machine Instance (AMI). Workshop participants will be given information on how to log-in to the AMI during the workshop. Learners using these materials for self-directed study will need to set up their own AMI. Information on setting up an AMI and accessing the required data is provided on the Metagenomics Workshop Setup page.

For Instructors

If you are teaching this lesson in a workshop, please see the Instructor notes.

This is the second lesson of the Metagenomics Workshop comprised of four lessons in total.

Lesson Reference

This page and the six episodes in this lesson are adapted from Introduction to the Command Line for Genomics lesson.

Citation

Please cite as:

Claudia Zirión Martínez; Diego Garfias Gallegos; Tania Vanessa Arellano Fernández; Aarón Espinosa Jaime; Edder D Bustos Díaz; José Abel Lovaco Flores; Luis Gerardo Tejero Gómez; J Abraham Avelar Rivas; Nelly Sélem (March , 2023) A Data Carpentry- Style Metagenomics Workshop

	Setup	Download files required for the lesson
00:00	1. Introducing the Shell	What is a command shell and why would I use one? How can I move around in a computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer?
00:30	2. Navigating Files and Directories	How can I perform operations on files outside of my working directory? What are some navigational shortcuts I can use to make my work more efficient?
01:20	3. Working with Files and Directories	How can I view and search file contents? How can I create, copy and delete files and directories? How can I control who has permission to modify a file? How can I repeat recently used commands?
02:05	4. Redirection	How can I search within files? How can I combine existing commands to do new things?
02:50	5. Writing Scripts and Working with Data	How can we automate a commonly used set of commands? How can we transfer files between local and remote computers?
03:30	6. Project Organization	How can I organize my file system for a new bioinformatics project? How can I document my work?
04:00	Finish

Introduction to the Command Line for Metagenomics

Getting Started

For Instructors

Lesson Reference

Citation

Schedule