Detection of viral contamination in cell lines using ViralCellDetector.

ABSTRACT:

Background and aims

Cell lines are widely used in biomedical research to investigate various biological processes, including gene expression, cancer progression, and drug responses. However, cross-contamination with bacteria, mycoplasma, and viruses remains a persistent challenge. While the detection of bacterial and mycoplasma contamination is relatively straightforward, identifying viral contamination is more difficult. To address this issue, we developed ViralCellDetector, a tool designed to detect viral contamination by mapping RNA-seq data to a comprehensive viral genome library.

Methods

ViralCellDetector processes RNA-seq data from any host species by first aligning reads to the host reference genome, followed by mapping the unmapped reads to the NCBI viral genome data

SUBMITTER: Shankar R 

PROVIDER: S-EPMC12380829 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature