dorra28/metatranscriptomic-covid19-tunisia-

# Uncovering COVID-19 Dynamics in Tunisian Patients: A Meta-Transcriptomic Approach Reproducible bioinformatics pipeline accompanying the manuscript *"Uncovering COVID-19 Dynamics in Tunisian Patients: A Meta-Transcriptomic Approach"* (submitted to *Scientific Reports*). > **Authors:** Dorra Rjaibi, Oussama Souiai, Lilia Romdhane — Institut Pasteur de Tunis This repository contains the scripts used to process paired-end metatranscriptomic sequencing data from nasopharyngeal swabs of Tunisian COVID-19 patients (severe, moderate, and RT-PCR-negative controls) for three parallel analyses: 1. **Virus analysis** — SARS-CoV-2 genome mapping, assembly, lineage/clade assignment, and variant calling 2. **Host transcriptional response** — differential gene expression and functional/pathway enrichment 3. **Microbiome profiling** — taxonomic classification and alpha diversity of the nasopharyngeal microbiome --- ## Study overview - **Samples:** 34 Tunisian nasopharyngeal swab (NPS) samples (Severe n=9, Moderate n=14, Negative n=11), collected November 2021–January 2022 (Omicron-dominant period) - **Ethics approval:** Institut Pasteur de Tunis Ethics Committee, ID 2021/20/I - **RNA extraction:** QIAamp Viral RNA Mini Kit (Qiagen), 140 µL input - **Sequencing:** Paired-end 100 bp, Illumina HiSeq X, ≥37.4 million read pairs/sample ## Pipeline overview ``` ┌────────────────────┐ │ Raw FASTQ files │ └─────────┬───────────┘ │ ┌──────────────▼───────────────┐ │ A. Preprocessing │ │ FastQC → MultiQC → Cutadapt │ └──────────────┬───────────────┘ │ ┌──────────────────────────┼──────────────────────────┐ │ │ │ ┌───────▼────────┐ ┌──────────▼──────────┐ ┌──────────▼──────────┐ │ B. Virus │ │ C. Host response │ │ D. Microbiome │ │ analysis │ │ │ │ profiling │ │ │ │ │ │ …