2024–present · Bioinformatician / Research Collaborator
VIRALL — viral detection and characterization across sequencing platforms
A workflow for viral detection and characterization that scales across sequencing platforms, applied to viral reactivation studies in Alzheimer’s disease.
Problem
Detecting and characterizing viral sequences across heterogeneous sequencing platforms is difficult: tools differ per platform, and viral signal is often sparse against host background. Viral reactivation is increasingly implicated in Alzheimer’s disease, but reproducible detection pipelines are lacking.
Approach
Developed VIRALL, a workflow that processes raw reads to assemble contigs, identify viral sequences, classify and annotate viruses, assess assembly quality, and quantify abundance. It supports Nanopore, PacBio, Illumina paired/single-end, DNA-seq, RNA-seq, hybrid, and scRNA-seq datasets, with simple installation and execution on Linux.
Result
VIRALL provides a single reproducible path from raw reads to annotated viral abundance, and is being applied to viral reactivation studies in Alzheimer’s disease within the NASA OSDR Brain Analysis Working Group.
Collaboration with the NASA Open Science Data Repository (OSDR) Brain Analysis Working Group, Viral Reactivation subgroup.