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

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 i

SUBMITTER: Petkau A 

PROVIDER: S-EPMC5628696 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature