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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.

Cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

License

Free to use and open source under MIT License

Available

  • Puhti: 3.2, 3.4, 3.5, 4.6

Usage

On Puhti, the latest version of Cutadapt can be taken in use by loading the module:

module load cutadapt

You can check the available versions with the command:

module spider cutadapt

You can load a specific version with the command:

module load cutadapt/3.2

The basic syntax is:

cutadapt --help

Cutadapt should be run either in an interactive session or as a batch job.

Support

CSC Service Desk

More information

More information about Cutadapt can be found from the Cutadapt home page.