Custom R scripts and SLURM workflows for analysis of PRJEB81739 Illumina WGS data

This repository contains all custom R scripts, SLURM shell scripts, and supporting data used to analyze the whole-genome sequencing data of *Plasmodium falciparum* isolates under BioProject PRJEB81739. The workflows include variant calling, coverage analysis, SNP annotation, population structure, GWAS, and diversity metrics such as Tajima’s D.

Each script is provided in reproducible R Markdown format, and all rendered outputs are included. SLURM job submission scripts and function libraries are also provided for reproducibility. All files are documented and versioned.

This deposit complements the manuscript submitted to *Communications Biology*.