17 Overview

This chapter contains instructions for the SARS-CoV-2 sequencing data FastQC analysis with Galaxy on AnVIL activity.

Galaxy is a free computing platform that allows users to upload or “fetch” data from online repositories and analyze that data with supported tools using a point and click user interface (UI) rather than with a command-line interface. Galaxy on AnVIL means that the benefits of AnVIL (such as secure data sharing, access to controlled access data) are combined with the benefits of running a reproducible analysis with Galaxy.

Like all compute on AnVIL, Galaxy on AnVIL will incur costs.

17.1 Learning Objectives

This activity will teach you how to use the AnVIL platform to:

  1. Launch Galaxy on AnVIL
  2. Import data into Galaxy on AnVIL
  3. Examine sequence data files (.fastq files)
  4. Find, open, and run a tool (FastQC)
  5. Examine the quality control summary report (Webpage)
  6. Export your results for future viewing
  7. Show how to shut down Galaxy on AnVIL
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