SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data

Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification, and outbreak surveillance. Identification of single nucleotide polymorphisms (SNPs) across the genome by alignment against a reference genome is the most high 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 Mycobacterium bovis in livestock and wildlife, the principal causative agent of TB in these populations in Ireland. 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.