Diamond

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:

  • Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
  • Frameshift alignments for long read analysis.
  • Low resource requirements and suitable for running on standard desktops or laptops.
  • Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

Diamond 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 Diamond:

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

  2. Load the Diamond module (current version is 2.0.15):

$ module load life-sciences/diamond
3. Initialize the Diamond environment:

$ diamond_init
4. Diamond can now be executed as advertised.

Performance Notes

The following flags should be set according to the resources requested a particular job:

  • The -p flag can be set to the number of cores requested for the job. However, only use this if absolutely necessary, as Diamond will auto-detect the number of cores available.
  • 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

Licensing Information

Primary citation

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