ArticleiMetaOmics2026
CGAS (Chloroplast Genome Analysis Suite): An automated python pipeline for comprehensive comparative chloroplast genomics.
Article in iMetaOmics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
3 authors.
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Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.