Trim Galore

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

Trim Galore is made available on the UFS HPC via a conda environment which can by loaded as a module.

UFS HPC Usage Example

Follow these steps to use Trim Galore:

1. Start a qwiz or qvnc session. If using a qvnc session, open the Terminal.

2. Load the Trim Galore module (current version is 0.6.7):

$ module load life-sciences/trim-galore

3. Initialize the Trim Galore environment:

$ trim-galore_init

4. Trim Galore can now be executed as advertised.

Performance Notes

Use the -j flag to set it to the number of cores requested for the job (The default is one core).

Recommended resources per session

• 1 Node
• Memory and number of cores will depend on dataset size

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

• No community guides are available.

Official site and documentation

• Site
• Manual

Licensing Information

• Trim Galore is free to use and distribute under the terms of the GNU General Public License v3.0

Primary citation

Felix Krueger, Frankie James, Phil Ewels, Ebrahim Afyounian, & Benjamin Schuster-Boeckler. (2021). FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo (0.6.7). Zenodo. https://doi.org/10.5281/zenodo.5127899

Please remember to cite any additional methods used.

External Guides and Resources

• If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za