We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue.
For help with VirusSeq, please email firstname.lastname@example.org
The source codes, detailed User Guide, related tools, fasta files for reference genomes (hg19, GIBV etc.), genome annotation files, and the paired-end (PE) RNA-Seq files from a test sample can be downloaded here.
VirusSeq takes FASTQ files (paired-end reads) as input. Please read User Guide for VirusSeq carefully before running VirusSeq. The detailed User Guide, related tools, reference genomes, annotation files, and shell scripts can be downloaded here. The PE FASTQ RNA-Seq files from a test sample to run VirusSeq for detection of viruses and their integration site can also be downloaded here.