MARPLE Diagnostics¶
Pipeline for analysis of stem rust and yellow rust reads. The bundle packages version 1.5.
Usage example¶
The following command can be executed in the terminal to load the bundle:
After the module is loaded, the reads can be copied to the correct directory in
~/marple/reads. The module makes the marple command available. The
marple_shell command can be used to access a shell in the bundle.
Performance notes¶
No performance notes available
Recommended resources per session¶
MARPLE should be run on a system with at least 128 GB of RAM and 16 threads. The RAxML and Samtools resource recommendations were used as no recommendations for MARPLE could be found.
Benchmarks¶
No benchmarks available.
Community guides and tutorials¶
- No community guides available.
Official site and documentation¶
Licensing information¶
MARPLE Diagnostics is licensed under the GPLv3 license.
Primary citation¶
Savva, L., Bryan, A., Vinopal, D. et al. A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity. BMC Genomics 26, 327 (2025). doi
Radhakrishnan, G.V., Cook, N.M., Bueno-Sancho, V. et al. MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens. BMC Biol 17, 65 (2019). doi
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