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Microb Genom. 2017 Jun 8;3(6):e000116. doi: 10.1099/mgen.0.000116. eCollection 2017 Jun 30.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.

Author information

1​National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
2​University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
3​Health Canada - Bureau of Microbial Hazards, Ottawa, ON K1A 0K9, Canada.
4​Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada.
5​Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
6​Dalhousie University, Halifax, NS B3H 4R2, Canada.
7​BC Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada.
8​Simon Fraser University, Burnaby, BC V5A 1S6, Canada.


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 or at


bacterial genomics; bioinformatics; genomic epidemiology; infectious disease surveillance; phylogenomics; single nucleotide variation detection

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