Keywords: R, Plasmids, Visualization, WGS, AMR,
Webpages:
https://cran.r-project.org/web/packages/Plasmidprofiler/index.html,
http://biorxiv.org/content/early/2017/03/28/121350.1 Summary: Comparative analysis of bacterial plasmids from short read whole genome sequencing (WGS) data 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
Plasmidprofiler, a pipeline that uses Galaxy and
R 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
Plasmidprofiler R package is available at
https://anaconda.org/bioconda/r-plasmidprofiler The
Plasmidprofiler 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.
