CGAS - Chloroplast Genome Analysis Suite

CGAS is organized into 14 modular components that collectively cover chloroplast genome assembly, annotation, comparative genomics, and phylogenetic analysis. Modules can be executed individually or combined into batch workflows, depending on the study design and data availability.Modules 1–4 serve as preparation steps. Module 1 performs batch processing of raw sequencing reads, including comprehensive quality assessment, adapter trimming, quality filtering, chloroplast genome assembly, and coverage depth analysis, and produces detailed summary reports. Module 2 annotates assembled chloroplast genomes from FASTA files using PGA, generating standardized GenBank files. Module 3 normalizes gene names and annotations across genomes to ensure consistency in downstream comparative analyses. Module 4 converts annotated GenBank files into FASTA and TBL formats suitable for NCBI submission.Modules 5–13 constitute the main comparative analysis workflow and can be executed together using a single command (cgas 5,6,7,8,9,10,11,12,13). These modules perform gene content comparison, generation of publication-ready gene tables, chloroplast genome structure analysis (LSC, SSC, and IR regions), codon usage and amino acid composition analyses, substitution profiling, intron structure comparison, simple sequence repeat (SSR) detection and classification, and nucleotide diversity estimation. All analyses are conducted in batch mode across multiple species and produce publication-ready outputs, including tables, figures, and aligned sequence matrices.Module 14 extends CGAS to phylogenetic analysis by constructing alignment matrices from complete genomes, protein-coding genes, introns, or intergenic regions and reconstructing maximum-likelihood trees using IQ-TREE. This module is typically run separately, particularly when outgroup taxa are not included in the comparative dataset.