FASTQ files are generated by high throughput sequencers and contain base call and quality information for sequence reads from a prepared DNA library. Understanding their structure and being able to extract pertinent information is a key first step to analyzing genomic data. This lesson explains the structure of FASTQ files and provides instruction on basic commands to help you manipulate the files for your needs.

Course Curriculum

  • 1

    Chapter 1: Getting Started

    • FASTQ File Format

    • The Command Line (Terminal for MAC OSX; Developer Tools for Windows 10 Anniversary Update)

    • Basic Unix Commands to Navigate in the Terminal Window (Command Line)

  • 2

    Chapter 2: Viewing FASTQ Files

    • Basic Commands in the Command Line to View FASTQ Files

About the instructor

Adjunct Professor, Environmental & Life Sciences Graduate Program, Trent University

Linda Rutledge

When I first started analysing genetic data, I was thankful that I had the support of fellow students and a really helpful post-doc nearby. It simply made learning more complex bioinformatics that much easier. But I wish I had an online source for information all in one place. As an educator, I have developed these interactive online lessons to help students learn and remember biological concepts. I am passionate about science and education, and I believe the effective transfer of knowledge is a key part of the scientific process. I've taught several traditional and online university biology courses, but I really wanted a more accessible, interactive, and mobile framework for learning. With that in mind, I am currently developing fully-responsive online courses that include computing for biologists, bioinformatics, and other concepts in biology.You can find out more about me at

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