PT  - JOURNAL ARTICLE
AU  - Adrian Zetner
AU  - Jennifer Cabral
AU  - Laura Mataseje
AU  - Natalie C Knox
AU  - Philip Mabon
AU  - Michael Mulvey
AU  - Gary Van Domselaar
TI  - Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data
AID  - 10.1101/121350
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 121350
4099  - http://biorxiv.org/content/early/2017/03/28/121350.1.short
4100  - http://biorxiv.org/content/early/2017/03/28/121350.1.full
AB  - 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-plasmidprofilerThe custom Plasmid Profiler R package is also available as a CRAN package at https://cran.r-project.org/web/packages/Plasmidprofiler/index.htmlGalaxy tools associated with the pipeline are available as a Galaxy tool suite at https://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504The source code is available at: https://github.com/phac-nml/plasmidprofilerThe Galaxy implementation is available at: https://github.com/phac-nml/plasmidprofiler-galaxyContact Email: gary.vandomselaar{at}canada.caAddress: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, CanadaSupplementary information Documentation: http://plasmid-profiler.readthedocs.io/en/latest/