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Warning!

Puhti and Mahti are being decommissioned in stages, and their storage areas will become fully unavailable from 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

FastQC

FastQC is a quality control tool for high-throughput sequence data.

License

Free to use and open source under GNU GPLv3.

Available

  • Puhti: 0.11.9
  • Chipster graphical user interface

Usage

To initialize on Puhti, use:

module load biokit

You can then run FastQC:

fastqc --help

If you run FastQC without command line arguments, it will open a GUI. The best way to run a GUI remotely on Puhti is to use the Puhti web interface desktop.

More information