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AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Hello, `amrfinder_update` does not respect `DEFAULT_DB_DIR` when build with `make DEFAULT_DB_DIR=somewhere` while `amrfinder -u` as it calls `exec (fullProg ("amrfinder_update") + " -d " + shellQuote (dbDir. getParent ()) +...
Once the output is created, it would be nice if a matrix 1/0 representing presence/absence for each gene is generated. Users could select minimum coverage and identity treshold for considering...
The `-u` (update) option does two things: 1. DOWNLOAD 2. FORMAT (`makeblastdb`) Could you please add an option to (re)-format the BLAST databases (CDS and Prot) as provided by the...
Hi guys, I am wondering how to propose new mutations in resistance genes which were reported in the last year, but are not yet included in the database ? Is...
Thanks for the thorough Wiki page on database files. For the point mutations listed in the Reference Gene Catalog, is there a way to get their position and derived allele...
Hi, First of all, thanks for the tool ! I wanted to have your insights on using the tool to screen viruses (bacteriophages) for AMR genes. Best,
Hi and thanks for developing and maintaining AMRFinder! We use AMRFinder within Bakta and we quite often get filed issues when people move their Bakta database containing an instance of...
Hello, For organisms that have point mutation detection supported, amr-finder-plus reports the amino acid change (e.g. S83F for QRDR mutations for Salmonella). Would it be possible to also report the...
Hi, new AMRfinderplus user - very useful tool, thanks! I may be missing something, but it appears that the only way to automatically download/build the database is through the amrfinder_update...
AMRProt
Updated my databse and new version of armfinder is not working: The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus: No...
