Main tool : staramr
Additional tools:
- mlst 2.23.0
- ncbi-blast+ 2.12.0+
- any2fasta 0.4.2
- Databases for PlasmidFinder, PointFinder, ResFinder
Database version information:
##### staramr db information at time of docker image build #####
resfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/resfinder
resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
resfinder_db_commit = c0aa05c5cae9da75e4395e9fa3dd5057e3bf4a75
resfinder_db_date = Tue, 09 Sep 2025 18:35
pointfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/pointfinder
pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
pointfinder_db_commit = 29d83a51cb41e429e38e46b1096608b9accb2b2a
pointfinder_db_date = Fri, 22 Aug 2025 09:34
pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus
pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella
plasmidfinder_db_dir = /usr/local/lib/python3.9/site-packages/staramr/databases/data/update/plasmidfinder
plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
plasmidfinder_db_commit = 49c24c1c9401fa175fbcfdbd4b37227a160baca4
plasmidfinder_db_date = Wed, 10 Sep 2025 18:56
mlst_version = 2.23.0
pointfinder_gene_drug_version = 070623
resfinder_gene_drug_version = 072423
STARAMR uses several databases that it does not maintain. As such, this image is re-built twice a year for the latest of these databases {latest-version}={date of rebuilding}.
Full documentation: https://github.com/phac-nml/staramr
staramr scans bacterial genome contigs for AMR genes and plasmids
# run "staramr search" on a genome assembly (broken into multiple lines for readability)
staramr search -o /data/staramrtest-Salmonella \
--pointfinder-organism salmonella \
--plasmidfinder-database-type enterobacteriales \
/data/salmonella_enterica_assembly.fasta
# to get database information
staramr db info