Genomics Workshop

Key Info
Description - a brief synopsis, abstract or summary of what the learning resource is about: 

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 nucleotide abbreviations and the concept of genomic variation within a population. 
Workshop Overview.  Workshop materials include a recommendation for a dataset to be used with the lesson materials.

Project organization and management:
Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
Introduction to the command line:
Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
Data wrangling and processing:
Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation.
Introduction to cloud computing for genomics:
Learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources.


Authoring Person(s) Name: 
Erin Becker
Authoring Organization(s) Name: 
Data Carpentry
License - link to legal statement specifying the copyright status of the learning resource: 
Creative Commons Attribution 4.0 International - CC BY 4.0
Access Cost: 
No fee
Citation - format of the preferred citation for the learning resource: 
Teal, Tracy, Becker, Erin, Freeman, Bob, Williams, Jason J, Reiter, Taylor, & Lapp, Hilmar. (2017, November). Data Carpentry Genomics Workshop Home Page (Version v2017.11.0). Zenodo.
Primary language(s) in which the learning resource was originally published or made available: 
More info about
Keywords - short phrases describing what the learning resource is about: 
Data archiving
Data formats
Data management
Data storage
Genomics data
Subject Discipline - subject domain(s) toward which the learning resource is targeted: 
Life Sciences: Genetics and Genomics
Life Sciences: Microbiology
Published / Broadcast: 
Wednesday, November 1, 2017
ID - identifier that provides the means to locate the learning resource or its citation: 
Type - namespace prefix for the citable locator, if any: 
Publisher - organization credited with publishing or broadcasting the learning resource: 
Data Carpentry
Version - revision or edition number or date associated with a learning resource: 
Media Type - designation of the form in which the content of the learning resource is represented, e.g., moving image: 
Interactive Resource - requires a user to take action or make a request in order for the content to be understood, executed or experienced.
Contact Person(s): 
Erin Becker
Educational Info
Purpose - primary educational reason for which the learning resource was created: 
Instruction - detailed information about aspects or processes related to data management or data skills.
Learning Resource Type - category of the learning resource from the point of view of a professional educator: 
Unit - long-range plan of instruction on a particular concept containing multiple, related lessons.
Target Audience - intended audience for which the learning resource was created: 
Data manager
Early-career research scientist
Graduate student
Mid-career research scientist
Research faculty
Research scientist
Intended time to complete - approximate amount of time the average student will take to complete the learning resource: 
More than 1 Day (but less than 1 week)