q2-rgi wraps the functionalities of the RGI tool, which is used to predict antibiotic resistomes from assembled sequences or reads based on homology and SNP models. The application uses reference data from the Comprehensive Antibiotic Resistance Database (CARD).
The CARD database provides comprehensive coverage of resistance mechanisms, including both clinical and experimental data. It also includes mechanisms with indirect contributions to resistance.
Installation¶
q2-rgi isn’t part of the MOSHPIT distribution and has to be installed separately. Please follow these installation instructions.
- Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., Edalatmand, A., Petkau, A., Syed, S. A., Tsang, K. K., Baker, S. J. C., Dave, M., McCarthy, M. C., Mukiri, K. M., Nasir, J. A., Golbon, B., Imtiaz, H., Jiang, X., Kaur, K., … McArthur, A. G. (2022). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D690–D699. 10.1093/nar/gkac920