NGS Data Analysis of Bean Yellow Mosaic Virus (BYMV)

This project contains the workflow, results, and reports from NGS analysis of BYMV (SRA ID: SRX7118692), performed on Galaxy.eu.

Tools Used

• FastQC, Trim Galore, MultiQC
• BWA-MEM2, SAMtools
• LoFreq for SNP calling
• Velvet, SPAdes for assembly
• IGV for visualization

Results Summary

• Initial mapping rate: 26.98%
• Post-duplicate removal: 37.59%
• SNPs identified via LoFreq
• De novo assembly validated with QUAST and BLAST

Folder Structure

• results/: Contains reports and summary files
• plots/: Visuals like FastQC plots or IGV screenshots
• scripts/: Command lines or workflow steps
• references/: Reference genome links or notes

Acknowledgment

Analysis was performed using the Galaxy.eu platform.