Difference between revisions of "Amrfinderplus"
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Latest revision as of 15:59, 27 May 2022
Description
NCBI has developed AMRFinderPlus, a tool that identifies AMR genes, resistance-associated point mutations, and select other classes of genes using protein annotations and/or assembled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinderPlus relies on NCBI’s curated Reference Gene Database and curated collection of Hidden Markov Models. For more information on how AMRFinderPlus operates, please see the Methods section of the AMRFinderPlus documentation. See our documentation for a description of all our NCBI antimicrobial resistance resources.
Environment Modules
Run module spider amrfinderplus to find out what environment modules are available for this application.
System Variables
- HPC_AMRFINDERPLUS_DIR - installation directory
- HPC_AMRFINDERPLUS_BIN - executable directory
Citation
If you publish research that uses amrfinderplus you have to cite it as follows:
Please cite Feldgarden, Michael, Vyacheslav Brover, Daniel H. Haft, Arjun B. Prasad, Douglas J. Slotta, Igor Tolstoy, Gregory H. Tyson et al. "Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates." Antimicrobial agents and chemotherapy 63, no. 11 (2019): e00483-19. https://pubmed.gov/31427293 in any work or product based on this material.