FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.

ABSTRACT: DNA viruses are important infectious agents known to mediate a large number of human diseases, including cancer. Viral integration into the host genome and the formation of hybrid transcripts are also associated with increased pathogenicity. The high variability of viral genomes, however requires the use of sensitive ensemble hidden Markov models that add to the computational complexity, often requiring > 40 CPU-hours per sample. Here, we describe FastViFi, a fast 2-stage filtering method that reduces the computational burden. On simulated and cancer genomic data, FastViFi improved the running time by 2 orders of magnitude with comparable accuracy on challenging data sets. Recently published methods have focused on identification of location of viral integration into the human host genome

SUBMITTER: Javadzadeh S 

PROVIDER: S-EPMC9041341 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature