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Abstract

Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification and outbreak surveillance. Identification of SNPs across the genome by alignment against a reference genome is the highest precision method of delineating strains. SNiPgenie is a bioinformatics pipeline designed to perform the entire variant calling process across many samples simultaneously. It was developed in the context of developing WGS tools to support the tracking of infection transmission of in livestock and wildlife, the principal causative agent of bovine tuberculosis in these populations. SNiPgenie may, however, be applied to other bacteria where evolutionary change can be tracked accurately using SNPs. The tool comes with both a command line and a user-friendly graphical interface. It can run on standard desktop or laptop computers. SNiPgenie and its documentation are available at https://github.com/dmnfarrell/snipgenie.

Funding
This study was supported by the:
  • Irish Department of Agriculture Food and the Marine (Award 2022PSS113)
    • Principal Award Recipient: StephenV Gordon
  • Irish Department of Agriculture Food and the Marine (Award 2019R404)
    • Principal Award Recipient: StephenV Gordon
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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/content/journal/acmi/10.1099/acmi.0.001021.v3
2025-09-22
2026-04-22

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