ViGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors.

ABSTRACT: An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expressi

SUBMITTER: Bhuvaneshwar K 

PROVIDER: S-EPMC5996193 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature