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+# Clinical and Bacterial Determinants of Unfavorable Tuberculosis Treatment Outcomes: An Observational Study in Georgia
+
+## Supplementary Material
+
+This repository contains the supplementary material for the study entitled 
+**"Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia"** 
+available as a non-reviewed pre-print in *medRxiv* [DOI: 10.1101/2025.01.20.25320828v1](https://www.medrxiv.org/content/10.1101/2025.01.20.25320828v1)
+
+The supplementary materials provided here include:
+
+- The complete dataset.
+- A step-by-step description of all analyses conducted using R Markdown documents.
+- Supplementary results 
+
+## Repository Structure
+
+### 1. `data/`
+This folder contains the data used in the study.
+
+- `georgia_all_cases.tsv` – The complete dataset of tuberculosis cases used in the analysis.
+- `toutcomes_all.treefile` – The phylogenetic tree file, inferred with IQ-TREE2, including *M. canettii* as outgroup.
+
+---
+### 2. `analysis/`
+Contains R Markdown scripts and supporting files for the analyses.
+
+#### Key files:
+- `toutcomes_analysis.Rmd` – The main script describing and performing the analysis of the study. 
+- `GWAS_analysis.Rmd` – Script containing the analysis of GWAS output files of pyseer.
+- `toutcomes_phylogeny.Rmd` – Script for plotting the phylogenetic tree shown in Figure 1.
+
+#### Subfolder: `GWAS/`
+This subdirectory holds data and results related to GWAS analyses.
+
+**Input files:**
+- `georgia_toutcomes.covariates` – Covariate data used in GWAS models (treatment outcome).
+- `georgia_toutcomes.pheno` – Phenotype data of tuberculosis patients (treatment outcome).
+- `georgia_toutcomes.sublineages` – Data on genetic sublineages used in the study (treatment outcome).
+
+**Results files (in `GWAS/results/`):**
+- `gtoutcomes.pyseer.mixed_effects.results.txt` – Results from mixed effects model on treatment outcomes.
+- `gtoutcomes.pyseer.mixed_effects.BURDEN.results.txt` – Burden analysis results for treatment outcomes.
+- `cavity.pyseer.mixed_effects.results.txt` – Results for the analysis of cavitary disease.
+- `cavity.pyseer.mixed_effects.BURDEN.results.txt` – Burden analysis for cavitary disease.
+- `infiltration.pyseer.mixed_effects.results.txt` – Results for infiltration disease manifestation.
+- `infiltration.pyseer.mixed_effects.BURDEN.results.txt` – Burden analysis for infiltration.
+- `disemination.pyseer.mixed_effects.results.txt` – Results for disease dissemination.
+- `disemination.pyseer.mixed_effects.BURDEN.results.txt` – Burden analysis for dissemination.
+- `Rv1462_nonsyn_90freq_mutations.tsv` – List of samples with fixed mutations in the *Rv1462 (sufD)* gene.
+
+#### Subfolder: `disease_manifestation/`
+Contains pyseer input data files used in GWAS models (disease manifestation).
+
+- `georgia_cavity.pheno` – Data on cavitary disease cases.
+- `georgia_infiltrate.pheno` – Data on infiltration cases.
+- `georgia_dissemination.pheno` – Data on dissemination cases.
+- `georgia_disman.covariates` – Covariate data.
+- `georgia_disman.sublineages` – Sublineage data.
+---
+
+### 3. `results/`
+This folder contains results for different anaylses. For models,
+it contains ROC-AUC and PR-AUC plots, forest plots, and tables with the results of the 
+associations. Additionally, it contains:
+
+- `EDA/summary_univariate_table.tsv` - Table with unadjusted odds ratios for all variables. 
+- `feature_selection/` – Results of feature selection.
+- `phylogeny/` – The phylogeny shown in Figure 1.
+- `imputed_toutcomes_all.tsv` – Final dataset with **imputed values** for TTP and BMI used for statistical analysis.
+---
+
+## Citation
+
+If you use this repository, please cite our pre-print available in *medRxiv*. [DOI: 10.1101/2025.01.20.25320828v1](https://www.medrxiv.org/content/10.1101/2025.01.20.25320828v1)
+
+---
+
+For any questions or issues related to this repository, please contact [Galo A. Goig](galo.goig@swisstph.ch)
+
+---