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

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Whole-genome sequencing (WGS) offers high-resolution insights into microbial pathogens, crucial for antibiotic resistance profiling, lineage classification, and outbreak surveillance.
• Accurate strain delineation relies on identifying single nucleotide polymorphisms (SNPs) through genome alignment against a reference.

Purpose of the Study:

• To develop SNiPgenie, a bioinformatics pipeline for simultaneous variant calling across multiple samples.
• To support the tracking of *Mycobacterium bovis* infection transmission in livestock and wildlife.

Main Methods:

• SNiPgenie automates the entire variant calling process for single nucleotide polymorphisms (SNPs).
• The pipeline was developed for analyzing whole-genome sequencing (WGS) data.
• It offers both command-line and graphical user interfaces and runs on standard computers.

Main Results:

• SNiPgenie enables high-precision delineation of microbial strains using SNPs.
• The pipeline facilitates simultaneous variant calling across numerous samples.
• It is applicable to various bacterial species for tracking evolutionary changes.

Conclusions:

• SNiPgenie is an efficient tool for whole-genome sequencing analysis and SNP identification.
• The pipeline supports epidemiological surveillance and understanding of pathogen transmission dynamics.
• It provides a user-friendly and accessible solution for bacterial genomics research.