CGAS (Chloroplast Genome Analysis Suite): An automated python pipeline for comprehensive comparative chloroplast...

Chloroplast Genome Analysis Suite (CGAS) is a comprehensive bioinformatics pipeline that streamline chloroplast genome analysis from raw sequencing reads to publication-ready outputs. The suite integrates 14 specialized modules organized across three sequential phases. Phase 1 (Modules 1-4) handles genome assembly, quality control, annotation, gene normalization, and National Center for Biotechnology Information-format conversion using tools such as fastp, GetOrganelle, PGA, and others. Phase 2 (Modules 5-13) enables batch comparative genomics, encompassing gene content comparison, genome structure characterization, codon usage analysis, amino acid composition, single-nucleotide polymorphism detection, intron profiling, simple sequence repeat identification, and nucleotide diversity assessment-with R-based visualizations integrated where graphical representation of results is required. Phase 3 (Module 14) performs robust phylogenetic inference via alignment and tree-building programs, including MAFFT, MACSE, IQ-TREE, and others. Together, CGAS transforms raw chloroplast genome data into comparative insights, providing researchers with an automated, reproducible, and scalable solution for comparative chloroplast genomics, available at https://github.com/abdullah30/Chloroplast-Genome-Analysis-Suite-CGAS.