Iyunoluwa-J/Ethiopian_oral_cancer_microbiome

Script for the data wrangling and clean up for the Ethiopian oral cancer microbiome project **Ethiopian Oral Cancer Microbiome Project – Data Processing Overview** This repository contains scripts and workflows for the data wrangling, decontamination, and downstream cleanup of all microbiome samples used in the Ethiopian Oral Cancer Microbiome Project. All steps were developed and executed by Iyunoluwa Ademola-Popoola. The pipeline brings raw QIIME2 feature tables and representative sequences through a series of merging, decontamination, filtering, and cleanup steps to produce the final dataset for analysis. **Data_wrangling.txt** Script for merging feature tables and representative sequences, assigning taxonomy, building a phylogenetic tree, and preparing inputs for decontamination. **decontam.R** R script for identifying and filtering contaminants from the feature table using the decontam package. **downstream_cleanup.txt** Annotated shell script (QIIME2-based) for filtering controls, excluding problematic samples, removing duplicates, and cleaning non-bacterial features (chloroplasts, mitochondria).