Whole-genome automated assembly pipeline for <i>Chlamydia trachomatis</i> strains from reference, <i>in vitro</i> and clinical samples using the integrated CtGAP pipeline.

ABSTRACT: Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with in vitro propagation. No single tool exists for the entirety of Ct genome assembly, necessitating the adaptation of multiple programs with varying success. Compounding this issue is the absence of reliable Ct reference strain genomes. We, therefore, developed CtGAP-Chlamydia trachomatis

SUBMITTER: Olagoke O 

PROVIDER: S-EPMC11704784 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature