CtGAP 2.0: enhanced genome assembly, strain resolution, and phylogenomics for <i>Chlamydia trachomatis</i>

We present <i>Chlamydia trachomatis</i> Genome Assembly Pipeline (CtGAP) 2.0, an enhanced version of CtGAP, that provides a seamless installation process-eliminating the need for multiple standalone tools-and a streamlined command-line interface, introduces automatic assembly quality scoring and selection for downstream analyses, and integrates chromosome and plasmid typing along with phylogenomics.