EzClermont

EzClermont: In silico Escherichia coli phylotyping using the Clermont PCR scheme

EzClermont implements an in silico adaptation of the Clermont PCR method to assign phylogroups to Escherichia coli strains directly from genome assemblies without laboratory PCR.

Key Features:

• In Silico Clermont PCR Simulation: Reproduces the traditional Clermont PCR phylotyping scheme computationally using genome assembly data.
• High-Throughput Genome Processing: Processes large collections of genome assemblies for scalable phylogroup assignment.
• Versioned Implementation: Maintained under version control (e.g., version 0.4.0) to ensure reproducibility and analytical consistency.

Scientific Applications:

• E. coli Phylogroup Classification: Determines phylogenetic groups of Escherichia coli isolates for microbial ecology, epidemiology, and pathogenesis studies using whole-genome data.
• Comparative Genomics: Enables rapid phylogenetic stratification of isolates in large-scale genomic analyses.

Methodology:

EzClermont computationally simulates primer detection and amplicon prediction defined in the Clermont PCR scheme against assembled genome sequences to infer phylogroup assignments consistent with the established experimental protocol.