VIRTUS3¶
Description¶
VIRTUS3 enables the detection and quantification of viral transcripts in scRNA-seq experiments. For example, VIRTUS3 can be used to identify cells infected with EBV and also measure viral gene expression at single-cell resolution. It achieves this by leveraging Cell Ranger for human transcriptome analysis and cell identification, then quantifies unmapped reads against viral references. VIRTUS3 exclusively quantifies reads that do not align to the human transcriptome, thereby minimizing false positives arising from ambiguous reads with similarity to both human and viral genomes. Additionally, Cell Ranger is not optimal for assessing viral transcripts because it discards reads that map to multiple genes, whereas viral genomes are compact and extensively overlapping. VIRTUS3 overcomes this by using quasi-alignment to enable accurate viral transcript quantification.
Environment Modules¶
Run module spider virtus3 to find out what environment modules are available for this application.
Environment Variables¶
- HPC_VIRTUS3_DIR - installation directory
- HPC_VIRTUS3_BIN - executable directory
- HPC_VIRTUS3_REF - reference data directory
Categories¶
bioinformatics, genomics, rna-seq