TY - JOUR T1 - SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology JF - bioRxiv DO - 10.1101/092940 SP - 092940 AU - Aaron Petkau AU - Philip Mabon AU - Cameron Sieffert AU - Natalie Knox AU - Jennifer Cabral AU - Mariam Iskander AU - Mark Iskander AU - Kelly Weedmark AU - Rahat Zaheer AU - Lee S. Katz AU - Celine Nadon AU - Aleisha Reimer AU - Eduardo Taboada AU - Robert G. Beiko AU - William Hsiao AU - Fiona Brinkman AU - Morag Graham AU - the IRIDA Consortium AU - Gary Van Domselaar Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/12/10/092940.abstract N2 - Motivation The 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.Results SNVPhyl (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.Availability SNVPhyl 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. ER -