PlasmidFinder

PlasmidFinder is a bioinformatics tool designed to identify and annotate plasmids in bacterial genomes. It is particularly useful in the context of antimicrobial resistance (AMR) surveillance, as many plasmids carry genes that confer resistance to antibiotics. PlasmidFinder uses a reference database of known plasmids, which includes information on their sequences and associated resistance genes. The tool employs a combination of sequence alignment and homology search algorithms to detect the presence of plasmids in query genomes. It can process both complete genomes and contigs generated from short-read sequencing data. PlasmidFinder is open-source and freely available, making it accessible to researchers and clinicians worldwide. The tool has been widely adopted in the scientific community and has contributed to the understanding of plasmid-mediated AMR. However, like any bioinformatics tool, PlasmidFinder has limitations, including potential false positives and negatives, and its accuracy depends on the quality and completeness of the input data. Users are encouraged to validate the results with experimental data. PlasmidFinder is part of the Pathogen Watch suite of tools, which also includes tools for identifying other mobile genetic elements and AMR genes.