anvi-setup-amrfinder
Table of Contents
Downloads and sets up NCBI's AMRFinderPlus database for anvi-run-amrfinder.
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Authors
Requires
This program seems to know what its doing. It needs no input material from its user. Good program.
Provides
Usage
This program downloads and sets up NCBI’s AMRFinderPlus database for use with anvi-run-amrfinder. It produces an amrfinder-data artifact.
We have not included AMRFinderPlus as a part of the standard anvi’o installation, so if you want to use it you first need to install it into your anvi’o environment:
conda install -c conda-forge -c bioconda ncbi-amrfinderplus
Basic usage
anvi’o uses AMRFinderPlus’s own program, amrfinder_update, to download the newest version of the database from NCBI:
anvi-setup-amrfinder
Custom data directory
By default, anvi’o stores the database at anvio/data/misc/AMRFinder/. If you want to store it in a different location you can use:
anvi-setup-amrfinder --amrfinder-data-dir path/to/directory
In case you already have an AMRFinderPlus database on your computer or your computer cluster, you can direct anvi’o to it using anvi-run-amrfinder with --amrfinder-data-dir.
Updating the database
There are regular updates by NCBI to the AMRFinderPlus database and if you want to make sure that you are using the latest one you can replace the ‘old’ database in the default location with the newest version by running:
anvi-setup-amrfinder --reset
Anvi’o wants to avoid deleting valuable data in a non-default directory or to reset a database that may be shared with others, therefore you can only use the --reset flag for the default directory location. If you set up the database with --amrfinder-data-dir, you need to remove that directory yourself before setting it up again.
anvi-run-amrfinder records the database version in every contigs-db it annotates, so you can always find out which version you used with anvi-db-info.
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-setup-amrfinder.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.