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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 computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti login nodes and storage services are planned to remain available until 15 October 2026.

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