cano-wgMLST_BacCompare

cano-wgMLST_BacCompare performs whole-genome multilocus sequence typing (wgMLST)-based comparative analyses to assess genetic relatedness and identify discriminatory genes among bacterial strains for epidemiological and comparative genomic studies.

Key Features:

• Whole-Genome Sequence-Based Comparisons: Performs comprehensive whole-genome comparisons derived from next-generation sequencing data.
• Extended MLST Approaches: Implements extended multilocus sequence typing (MLST) approaches with emphasis on whole-genome MLST (wgMLST).
• Canonical wgMLST Tree Construction: Constructs a canonical wgMLST (cano-wgMLST) tree by integrating wgMLST-constructed tree topology with a feature selection approach to identify and visualize genes that differ at each tree split.
• Comparative Genomic Analysis: Identifies and displays gene differences between bacterial strains to highlight functions related to virulence and pathogenicity.
• Demonstrated Datasets: Has been applied to datasets of 22 Campylobacter jejuni isolates and 59 Salmonella Heidelberg isolates.

Scientific Applications:

• Epidemiological Investigations: Assess genetic relatedness among bacterial strains to support outbreak investigation and transmission inference.
• Comparative Genomic Analyses: Identify and study gene variations that may influence bacterial pathogenicity and virulence.
• Public Health Genomic Surveillance: Inform analyses of genetic factors underlying bacterial outbreaks and strain differentiation.

Methodology:

Uses whole-genome multilocus sequence typing (wgMLST) and extended MLST approaches and constructs canonical wgMLST (cano-wgMLST) trees by integrating wgMLST-constructed tree topology with a feature selection approach to identify and visualize discriminatory genes at each split.