mercyoluwadarasimi/rotavirus-genomic-epidemiology-africa

A reproducible workflow for the genomic epidemiology and evolutionary analysis of Rotavirus A in Africa using publicly available whole-genome sequencing data. # Rotavirus Genomic Epidemiology in Africa A reproducible workflow framework for the genomic epidemiology and evolutionary analysis of Rotavirus A in Africa using publicly available whole-genome sequencing data. ## Overview Rotavirus A (RVA) is a major cause of acute gastroenteritis among children under five years of age, particularly in low- and middle-income countries. Genomic surveillance provides important insights into viral diversity, genotype distribution, reassortment events, and evolutionary dynamics. This project establishes a reproducible bioinformatics framework for the analysis of Rotavirus A whole-genome sequencing datasets from Africa. The workflow integrates sequence data acquisition, quality assessment, genomic characterization, phylogenetic analysis, and evolutionary interpretation. ## Objectives This project aims to: - Characterize the genomic diversity of Rotavirus A strains circulating in Africa. - Investigate genotype distribution and genetic variation among African Rotavirus A strains. - Explore evolutionary relationships using phylogenetic approaches. - Develop a reproducible computational workflow for rotavirus genomic surveillance. ## Data Sources This project uses publicly available Rotavirus A whole-genome sequencing datasets obtained from international nucleotide sequence repositories. Potential data sources include: - National Center for Biotechnology Information (NCBI) - European Nucleotide Archive (ENA) - Other publicly available genomic databases ## Bioinformatics Workflow The planned workflow includes: 1. Data acquisition and organization 2. Sequence quality assessment 3. Read preprocessing and quality control 4. Genome assembly and/or sequence processing 5. Genomic characterization and genotype assignment 6. Multiple sequence alignment 7. Phylogenetic analysis 8. Evolutionary analysis 9. Data visualization and reporting ## Repository Structure and Reproducibility This repository is organized to support transparent a …