RT Journal Article
SR Electronic
T1 SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 092940
DO 10.1101/092940
A1 Aaron Petkau
A1 Philip Mabon
A1 Cameron Sieffert
A1 Natalie Knox
A1 Jennifer Cabral
A1 Mariam Iskander
A1 Mark Iskander
A1 Kelly Weedmark
A1 Rahat Zaheer
A1 Lee S. Katz
A1 Celine Nadon
A1 Aleisha Reimer
A1 Eduardo Taboada
A1 Robert G. Beiko
A1 William Hsiao
A1 Fiona Brinkman
A1 Morag Graham
A1 the IRIDA Consortium
A1 Gary Van Domselaar
YR 2016
UL http://biorxiv.org/content/early/2016/12/09/092940.abstract
AB 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.