Metagenomic Identification and Variant Analysis of a Viral Genome
Developed a viral genome analysis pipeline on a High-Performance Computing (HPC) cluster to identify a mystery virus from Nanopore sequencing data. Performed metagenomic classification, genome alignment, coverage analysis, and variant detection using Centrifuge, Minimap2, Samtools, and Bcftools. Used Linux, Bash scripting, SLURM, and Git/GitHub to automate and manage the workflow. Successfully identified Lone Star virus (Bandavirus amblyommae), reconstructed its three-segment genome, and analyzed genomic variants.
GitHub Repository
Technologies
- Linux
- Bash
- HPC Cluster
- SLURM
- Centrifuge
- Minimap2
- Samtools
- Bcftools
- Nanopore Sequencing