ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks.…
Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for…
DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db.…
Route microbial / genome mining after assembly or binning: BGCs (antiSMASH, BiG-SCAPE), AMR (RGI, DeepARG, ResFinder), mobile elements (geNomad, VirSorter2, CheckV, mobileOG-db, ISEScan, IntegronFinder, MOB-suite, CGE Finders), antimicrobial peptides…
mlst — chromosomal multilocus sequence typing of assemblies against PubMLST schemes (Torsten Seemann wrapper). Use for isolate / HQ-MAG species ST calling. Upstream: https://github.com/tseemann/mlst. Route via cge-finders / microbial-mining for isolate…
PlasmidFinder — CGE in silico replicon / plasmid typing from assemblies or reads (BLAST/KMA vs PlasmidFinder DB). Use for Inc/replicon markers on isolates and HQ genomes. Upstream: https://github.com/genomicepidemiology/plasmidfinder. Route via cge-finders /…
pMLST — plasmid multilocus sequence typing from assemblies or reads using CGE / PubMLST plasmid schemes (IncI1, IncF, IncHI2, …). Use after PlasmidFinder replicon hits when a scheme ST is needed. Upstream: https://github.com/ssi-dk/pmlst (pmlst_ssi). Route…
ResFinder — CGE identification of acquired antimicrobial resistance genes (and optional PointFinder chromosomal mutations / DisinFinder biocide genes) from assemblies or reads. Use for isolate resistome typing with ResFinder DB phenotype mapping. Upstream:…