Data Carpentry lesson to learn how to use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation. A lot of genomics analysis is done using command-line tools for three reasons: 1) you will often be working with a large number of files, and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks, 2) you will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface, and 3) you will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if in fact a GUI tool even exists). In a previous lesson, you learned how to use the bash shell to interact with your computer through a command line interface. In this lesson, you will be applying this new knowledge to carry out a common genomics workflow - identifying variants among sequencing samples taken from multiple individuals within a population. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, aligning those reads to a reference genome, and ending by identifying and visualizing variations among these samples. As you progress through this lesson, keep in mind that, even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatic tools. What you learn here will enable you to use a variety of bioinformatic tools with confidence and greatly enhance your research efficiency and productivity.

This open education resource is a collection of collection of Concepts of Operating Systems in Question & Answer form that are useful as out-of-class activity while flipping the classroom.

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: 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.

Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards with genomics data. 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.

Software Carpentry lección para la terminal de Unix La terminal de Unix ha existido por más tiempo que la mayoría de sus usuarios. Ha sobrevivido tanto tiempo porque es una herramienta poderosa que permite a las personas hacer cosas complejas con sólo unas pocas teclas. Lo más importante es que ayuda a combinar programas existentes de nuevas maneras y automatizar tareas repetitivas, en vez de estar escribiendo las mismas cosas una y otra vez. El uso del terminal o shell es fundamental para usar muchas otras herramientas poderosas y recursos informáticos (incluidos los supercomputadores o “computación de alto rendimiento”). Esta lección te guiará en el camino hacia el uso eficaz de estos recursos.

Library Carpentry lesson to learn how to use the Shell. This Library Carpentry lesson introduces librarians to the Unix Shell. At the conclusion of the lesson you will: understand the basics of the Unix shell; understand why and how to use the command line; use shell commands to work with directories and files; use shell commands to find and manipulate data.

Software Carpentry lesson on how to use the shell to navigate the filesystem and write simple loops and scripts. The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.