pyMLST

pyMLST performs core genome multilocus sequence typing (cgMLST) analysis of bacterial whole-genome sequencing data for strain typing and outbreak investigation.

Key Features:

• Core Genome Database Creation: Supports creation or import of a core genome database tailored for cgMLST analysis.
• Flexible Input Options: Accepts assembler-generated draft genomes, raw sequencing data, and genomes from sequence databases, with a raw-data processing option called pyMLST-KMA.
• Alignment Methodology: For each gene, aligns the first allele against the bacterial genome using BLAT and aligns incomplete genes using MAFT (Multiple Alignment using Fast Fourier Transform).
• Data Management: Stores processed data in a SQLite database.

Scientific Applications:

• Pathogen Genome Evaluation: Evaluated on Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus genome collections.
• Outbreak Investigation: Used for allele-based cgMLST comparisons and generation of minimal spanning trees to inform bacterial outbreak analyses.

Methodology:

Creates or imports a core genome database; for each gene aligns the first allele to the genome with BLAT; aligns incomplete genes with MAFT; processes raw reads via pyMLST-KMA when used; stores results in a SQLite database; and generates minimal spanning trees for outbreak analyses.