CtGAP 2.0: enhanced genome assembly, strain resolution, and phylogenomics for Chlamydia trachomatis.

We present Chlamydia trachomatis 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.