Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST.

ABSTRACT: Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) and compared them with pyMLST, pyMLST-KMA, Ch

SUBMITTER: Biguenet A 

PROVIDER: S-EPMC10711306 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature