Summary: Comparative analysis of bacterial plasmids from whole genome sequence (WGS) data generated from short read sequencing is challenging. This is due to the difficulty in identifying contigs harbouring plasmid sequence data, and further difficulty in assembling such contigs into a full plasmid. As such, few software programs and bioinformatics pipelines exist to perform comprehensive comparative analyses of plasmids within and amongst sequenced isolates. To address this gap, we have developed Plasmid Profiler, a pipeline to perform comparative plasmid content analysis without the need for de novo assembly. The pipeline is designed to rapidly identify plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. The pipeline allows users to query plasmids for genes or regions of interest and visualize results as an interactive heat map. Availability and Implementation: Plasmid Profiler is freely available software released under the Apache 2.0 open source software license. A stand-alone version of the entire Plasmid Profiler pipeline is available as a Docker container at https://hub.docker.com/r/phacnml/plasmidprofiler_0_1_6/. The conda recipe for the Plasmid R package is available at: https://anaconda.org/bioconda/r-plasmidprofiler. The custom Plasmid Profiler R package is also available as a CRAN package at https://cran.r-project.org/web/packages/Plasmidprofiler/index.html. Galaxy tools associated with the pipeline are available as a Galaxy tool suite at https://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504. The source code is available at https://github.com/phac-nml/plasmidprofiler; the Galaxy implementation is available at https://github.com/phac-nml/plasmidprofiler-galaxy.
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