ArticleMicrobial genomics2017
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.
Article in Microbial genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- Stenotrophomonas maltophilia Bloodstream Infection Outbreak in Acute Care Hospital, California, USA, 2022-2023Emerging infectious diseases · 2026Review
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- Detection of Carbapenem-Resistant Bacteria in Skilled Nursing Facility Wastewater.The Journal of infectious diseases · 2026Article
- Phylogenomic analysis and genetic mechanisms of antifungal resistance in clinical isolates ofMicrobiology spectrum · 2026Article
- Plasmid genomic epidemiology ofMicrobial genomics · 2025Article
- Dogs fed raw meat-based diets are vectors of drug-resistant Salmonella infection in humans.Communications medicine · 2025Article
- A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens.The Lancet. Infectious diseases · 2025Review
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- Invasive Group A Streptococcus Hypervirulent M1Emerging infectious diseases · 2024Article
- refMLST: reference-based multilocus sequence typing enables universal bacterial typing.BMC bioinformatics · 2024Article
- Average Nucleotide Identity and Digital DNA-DNA Hybridization Analysis Following PromethION Nanopore-Based Whole Genome Sequencing Allows for Accurate Prokaryotic Typing.Diagnostics (Basel, Switzerland) · 2024Article
- Genomic Characterization of Three Canadian Mumps Outbreaks Demonstrates Endemic Transmission in Canada.Viruses · 2024Article
- Mutations inAntibiotics (Basel, Switzerland) · 2024Article
- Evaluation of Whole Genome Sequencing-Based Predictions of Antimicrobial Resistance to TB First Line Agents: A Lesson from 5 Years of Data.International journal of molecular sciences · 2024Article
- Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producingMicrobial genomics · 2024Article
- Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis.BMC genomics · 2024Article
- Characterization of MLST-99Microbiology (Reading, England) · 2024Article
- Pathogenomes of Shiga Toxin Positive and NegativeMicroorganisms · 2024Article
- Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producingFrontiers in microbiology · 2024Article
- Plasmid genomic epidemiology ofAntimicrobial agents and chemotherapy · 2023Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.