DiTing

DiTing is a bioinformatics pipeline used to infer and compare biogeochemical pathways from metagenomic and metatranscriptomic data sets.

DiTing 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 DiTing:

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

2. Load the DiTing module (current version is 0.9):

   $ module load life-sciences/diting
   

3. Initialize the DiTing environment:

   $ diting_init
   

4. DiTing can now be executed as advertised, for example (from the software documentation):

   $ diting.py -r Clean-reads_interleaved -o Clean-reads_interleaved.diting.out
   

Performance Notes

Recommended resources per session

According to the author of the pipeline, the recommended resources are:

• 1 Node with 8 cores (threads)
• 64 GB of RAM

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

• No community guides are available.

Official site and documentation

• Site
• Manual

Licensing Information

• DiTing is free to use and distribute under the terms of the GNU General Public Licence Version 3.0

Primary citation

Xue, C. X., Lin, H., Zhu, X. Y., Liu, J., Zhang, Y., Rowley, G., ... & Zhang, X. H. (2021). DiTing: a pipeline to infer and compare biogeochemical pathways from metagenomic and metatranscriptomic data. Frontiers in microbiology, 2118.

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