Knox, N. | bioRxiv Science

bioRxiv2017

Plasmid Profiler: Comparative Analysis Of Plasmid Content In WGS Data

SummaryComparative 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.\n\nAvailability and ImplementationPlasmid 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/.\n\nThe conda recipe for the Plasmid R package is available at: https://anaconda.org/bioconda/r-plasmidprofiler\n\nThe custom Plasmid Profiler R package is also available as a CRAN package at https://cran.r-project.org/web/packages/Plasmidprofiler/index.html\n\nGalaxy tools associated with the pipeline are available as a Galaxy tool suite at https://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504\n\nThe source code is available at: https://github.com/phac-nml/plasmidprofiler\n\nThe Galaxy implementation is available at: https://github.com/phac-nml/plasmidprofiler-galaxy\n\nContactEmail: gary.vandomselaar@canada.ca\n\nAddress: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada\n\nSupplementary informationDocumentation: http://plasmid-profiler.readthedocs.io/en/latest/

bioinformatics↗

bioRxiv2016

SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

MotivationThe recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research lab and into the front lines of surveillance and outbreak response requires user-friendly, reproducible, and scalable pipelines that have been well validated.\n\nResultsSNVPhyl (Single Nucleotide Variant Phylogenomics) is a bioinformatics pipeline for identifying high-quality SNVs and constructing a whole genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible, and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds, or in the presence of contamination.\n\nAvailabilitySNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.

bioinformatics↗