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  • Jessica Taylor
Data Wrangling and Processing for Genomics
Unrestricted Use
CC BY
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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.

Subject:
Computer Science
Information Science
Genetics
Measurement and Data
Material Type:
Module
Provider:
The Carpentries
Author:
Adam Thomas
Ahmed R. Hasan
Aniello Infante
Anita Schürch
dbmarchant
Dev Paudel
Erin Alison Becker
Fotis Psomopoulos
François Michonneau
Gaius Augustus
Gregg TeHennepe
Jason Williams
Jessica Elizabeth Mizzi
Karen Cranston
Kari L Jordan
Kate Crosby
Kevin Weitemier
Lex Nederbragt
Luis Avila
Peter R. Hoyt
Rayna Michelle Harris
Ryan Peek
Sheldon John McKay
Sheldon McKay
Taylor Reiter
Tessa Pierce
Toby Hodges
Tracy Teal
Vasilis Lenis
Winni Kretzschmar
Date Added:
08/07/2020
Introduction to the Command Line for Genomics
Unrestricted Use
CC BY
Rating
0.0 stars

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.

Subject:
Computer Science
Information Science
Genetics
Measurement and Data
Material Type:
Module
Provider:
The Carpentries
Author:
Amanda Charbonneau
Amy E. Hodge
Anita Schürch
Bastian Greshake Tzovaras
Bérénice Batut
Colin Davenport
Diya Das
Erin Alison Becker
François Michonneau
Giulio Valentino Dalla Riva
Jessica Elizabeth Mizzi
Karen Cranston
Kari L Jordan
Mattias de Hollander
Mike Lee
Niclas Jareborg
Omar Julio Sosa
Rayna Michelle Harris
Ross Cunning
Russell Neches
Sarah Stevens
Shannon EK Joslin
Sheldon John McKay
Siva Chudalayandi
Taylor Reiter
Tobi
Tracy Teal
Tristan De Buysscher
Date Added:
08/07/2020
Voices of Virginia: an Auditory Primary Source Reader
Conditional Remix & Share Permitted
CC BY-NC-SA
Rating
0.0 stars

Voices of Virginia pulls together stories from oral history collections from across decades and archives to create an all-audio source companion for Virginia’s high school and college students. The "album" is only two hours long, but contains dozens of short oral histories from eyewitnesses to key moments in American history, from the end of the Civil War to the 1980s. The excerpts are downloadable, accessible by smartphone, and accompanied by a transcript. Audio clips are also available on Soundcloud. You’ll also find a brief introduction to each narrator, historical context adapted from experts at Encyclopedia Virginia, American Yawp, and Public Domain sources, and helpful classroom tools like discussion questions, activities, and lesson plans that fit into both the Virginia high school and college U.S. History curriculum. By following the larger national story with narratives from across the Commonwealth, Voices of Virginia grounds students in how history guides and is guided by everyday people and their experiences.

This material is aligned to the History and Social Science Standards for Virginia Public Schools - March 2015.

The collection was curated by Jessica Taylor, Ph.D. with Emily Stewart.

Feedback regarding this collection is welcome at https://bit.ly/VoicesOfVirginia

Subject:
History
U.S. History
Material Type:
Activity/Lab
Lesson Plan
Primary Source
Reading
Provider:
Virginia Tech
Provider Set:
VTech Works
Author:
Emily Stewart
Jessica Taylor
Date Added:
03/23/2020