amrfinderplus_update
Tags: bacteria database antimicrobial-resistance update download ncbi sample-scope
Download and index the latest AMRFinder+ database.
Fetches the most recent AMRFinder+ databases from NCBI, indexes them, and packages them into a tarball.
This process is primarily used internally by Bactopia to build and update the built-in datasets.
Outputs
record (
db: Path,
logs: Set<Path?>
)
| Field | Type | Description |
|---|---|---|
db | Path | A compressed tarball of the latest AMRFinder+ database |
logs | Set<Path?> | Optional program specific log files |
Parameters
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
AMRFinderPlus
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob. Agents Chemother. (2019)
Source
Version
AMRFINDERPLUS_UPDATE:
- ncbi-amrfinderplus: 4.2.7