MSc_Dissertation_Kvass

Integrated 16S rRNA + shotgun metagenomics analysis of sourdough-based kvass fermentation. This project evaluates how dietary fibre supplementation impacts microbial composition and functional potential using reproducible workflows.

Project Highlights

• Multi-layer microbiome profiling (taxonomic + functional)
• Cross-tool comparison (QIIME2, MetaPhlAn4, Kraken2/Bracken, Kaiju)
• Functional interpretation (HUMAnN3, DRAM2)
• Reproducible folder structure from metadata to publication-ready figures

Repository Structure

• code/ — pipeline and analysis scripts
• metadata/ — manifests and sample annotations
• raw_data_links/ — references to raw/processed inputs
• results/ — processed outputs, figures, and summary tables

Workflow Overview

1. 16S processing (QIIME2): import → denoise → taxonomy → alpha/beta diversity
2. Shotgun taxonomy: MetaPhlAn4, Kraken2/Bracken, Kaiju
3. Functional profiling: HUMAnN3 and DRAM2
4. Visualization/reporting: R scripts for heatmaps, pathway summaries, and differential interpretation

Software Stack

• QIIME2 2024.2
• MetaPhlAn4, Kraken2, Bracken, Kaiju
• HUMAnN3, DRAM2
• R 4.3+ (ggplot2, pheatmap, vegan, etc.)
• Python 3.8+

Reproducibility Notes

• Tool-specific scripts are organized under each code/*/ directory.
• Input manifests are versioned under metadata/.
• Generated outputs are stored in structured subfolders under results/.
• This repository is intended as a traceable dissertation workflow archive.

Key Output Areas

• Diversity and composition trends across conditions
• Taxonomic agreement/disagreement across profilers
• Pathway and gene-family shifts associated with fibre treatment

Contact

For collaboration or role-related discussion, connect via GitHub profile: https://github.com/kavyamguru

Code Quality (SonarCloud)

• Config: sonar-project.properties (scans only `code/`).
• CI: .github/workflows/sonarcloud.yml runs on pushes/PRs to main/master.
• Required secrets in GitHub repo settings → Secrets and variables → Actions:
  • SONAR_TOKEN : SonarCloud project token.
• Default SonarCloud project identifiers:
  • organization: kavyamguru
  • projectKey & projectName: kavyamguru_MSc_Dissertation_Kvass.
• To run locally (optional): install sonar-scanner, export SONAR_TOKEN, then run sonar-scanner from repo root.