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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 adata sh12 requires user-friendly, reproducible and scalable pipelines that have been well validated. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible and scalable environment.

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SNVPhyl is able adata sh12 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 adata sh12 virtual machine images, and a Unix-based command-line application.

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SNVPhyl is released under the Apache 2. The widespread application of adata sh12 sequencing WGS to investigate infectious disease outbreaks has led to a proliferation of methods for classifying microbial samples based on genomic data.

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Single-nucleotide variant SNV -based methods have been especially useful and adata sh12 number of SNV phylogenomic pipelines are now available. However, these pipelines often operate under different execution environments, from locally installed command-line applications to web-based applications, and may require multiple analysis software for further processing of the resulting files.

We have developed Single Nucleotide Variant Phylogenomics SNVPhyl as an SNV-based phylogenomics pipeline that is integrated within the Galaxy platform providing a locally installable environment for phylogenomics analysis within adata sh12 larger-scale bioinformatics system. We demonstrate the successes and limitations of SNVPhyl under these scenarios, and provide guidance on identifying and handling problematic results.


The high-efficiency and cost-effectiveness of adata sh12 sequencing WGS using next-generation sequencing technologies is transforming the biomedical landscape. Entire microbial genomes can be rapidly sequenced and subsequently queried with nucleotide-level resolution, an exciting new ability that far outstrips other traditional microbial typing methods.

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