mihinduk/FRESH_cervicotype

Creation of the tools to determine more accurate cervicotypes for the South African FRESH cohort # FRESH Cervicotype Project **Multi-marker molecular profiling for species-level cervicovaginal community typing in South African women** ## Overview Standard 16S-based cervicovaginal community typing cannot resolve the species-level variation within diverse (non-*Lactobacillus*) communities that dominate in sub-Saharan African women, and this resolution gap obscures the biological mechanisms linking specific bacterial species, fungi, and Mollicutes to HIV acquisition risk. This project develops an integrated multi-marker approach (cpn60 + pheS + ITS + 16S + Mollicute-specific PCR) for species-level cervicotyping, applied to the FRESH cohort (Females Rising through Education, Support and Health) in Durban, South Africa. ## Project structure ``` FRESH_cervicotype/ ├── databases/ # Reference databases and classifiers │ ├── cpn60/ # cpnDB references, cpn60-Classifier training sets │ ├── pheS/ # Wuyts et al. framework + NCBI supplements │ ├── ITS/ # UNITE v10.0 classifier │ ├── 16S/ # SILVA/GG2 classifier + VALENCIA centroids │ ├── mollicute_primers/ # MgPa, M. hominis 16S, ureC primer sequences │ └── fredricks_bv_primers/ # BVAB1, BVAB2, Megasphaera, Fannyhessea primers ├── pipelines/ # Analysis pipelines │ ├── cpn60/ # DADA2 → cpn60-Classifier │ ├── pheS/ # DADA2 → custom pheS classifier │ ├── ITS/ # ITSxpress → DADA2 → UNITE │ ├── 16S/ # DADA2 → SILVA → VALENCIA │ └── integration/ # Multi-marker merge and cervicotype assignment ├── validation/ # Testing with public datasets │ ├── public_data/ # Downloaded SRA data (gitignored) │ └── results/ # Validation outputs ├── docs/ # Documentation │ ├── study_plan/ # Study plans and rationale │ └── background/ …