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

## TL;DR

CtGAP 2.0 is an improved tool for analyzing Chlamydia trachomatis genomes, offering better assembly, strain resolution, and phylogenomics.

## Contribution

CtGAP 2.0 introduces a unified installation, automatic quality scoring, and integrated typing and phylogenomics for Chlamydia trachomatis.

## Key findings

- CtGAP 2.0 simplifies the workflow by eliminating the need for multiple standalone tools.
- The tool includes automatic assembly quality scoring to improve downstream analysis accuracy.
- It integrates chromosome and plasmid typing with phylogenomics for comprehensive genomic analysis.

## Abstract

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.