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fatsp

fastp provides all-in-one preprocessing for FastQ files. The fastp bundle packages version 0.23.2.

UFS HPC Usage Example

The following command can be executed in the terminal to load the bundle:

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module load fastp
The fastp command can be run as shown as below: 
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fastp
The fastp_shelli command can be run for a shell in the fastp bundle. 
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fastp_shell

Performance Notes

No performance notes available

No recommended resources available

Benchmarks

No benchmarks available.

UFS HPC Community Guides and Tutorials

  • No community guides available.

Official site and documentation

Licensing Information

fastp is licensed under the MIT license.

Primary citation

  • Shifu Chen. 2023. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2: e107. https://doi.org/10.1002/imt2.107
  • Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884?i890, https://doi.org/10.1093/bioinformatics/bty560

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