SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
Petkau, Aaron and Mabon, Philip and Sieffert, Cameron and Knox, Natalie C. and Cabral, Jennifer and Iskander, Mariam and Iskander, Mark and Weedmark, Kelly and Zaheer, Rahat and Katz, Lee S. and Nadon, Celine and Reimer, Aleisha and Taboada, Eduardo and Beiko, Robert G. and Hsiao, William and Brinkman, Fiona and Graham, Morag and Van Domselaar, Gary,, 3, e000116 (2017),
doi = https://doi.org/10.1099/mgen.0.000116,
publicationName = Microbiology Society,
issn = ,
abstract= 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 laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is a bioinformatics pipeline for identifying high-quality single-nucleotide variants (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. 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.,
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