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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. {: .prereq}

For Instructors

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

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: DOI

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