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A quality control tool for high throughput sequence data.

FastQC requires an environment module

In order to use FastQC, you must first load the appropriate environment module:

module load fastqc

FastQC is a bioinformatics quality control program which is designed for use with high-throughput sequencer data. It's main purpose is to provide tools to give the user an idea of the quality of raw data coming out of a sequencer or sequence pipeline.


You will need to either use Open OnDemand or start a graphical SSH connection to use Ncview

Starting FastQC using Open OnDemand#

  1. On the bar at the top of the screen click Interactive Apps > Desktop
  2. Change parameters to:
    • Number of hours: 1 (or however long you need to run)
    • Number of cores: 4
    • Amount of memory requested: 16G
    • Number of nodes: 1
    • Partition: genacc_q (or whatever Slurm account/partition you prefer to use)
  3. Click the Launch button
  4. You'll be directed to a new screen, that will have a card labeled Desktop and Queued
  5. Once your Session starts, Click Launch Desktop
  6. Click Terminal (Black Square in Bottom Dashboard)
  7. Load the module fastqc using the command

Using FastQC#

Details on running FastQC can be found on the web: * in this tutorial video * on the Babraham Bioinformatics site

Last update: June 20, 2023