twylie/virosearch repository overview

⁠ViroSearch

We have designed and implemented a computational pipeline called ViroSearch for the automated search and characterization of variant virus sequences of potential biological interest within large-scale genomic data sets. As an example of the utility of ViroSearch, we analyzed Epstein Barr Virus (EBV) associated sequence variants within 81 samples (42 EBV-positive) derived from patients with post-transplant lymphoproliferative disorders (PTLDs). PTLDs have high morbidity and mortality rates, but it is not clear what clinical or epidemiological features associate with poor outcomes. As part of the ongoing NIH-funded PTLD-MSMS study of several hundred PTLD tissues, our goal is to apply ViroSearch in determining whether EBV sequence variants associate with specific clinical outcomes. In this initial analysis, we demonstrate that ViroSearch can identify EBV genomic variants, annotate them, and compare to known variants with published biological functions.

⁠Code and Documentation

https://github.com/twylie/virosearch⁠