Fig. 1

The overall workflow of VirTect. After mapping or remapping of short reads to the human and virus genome, VirTect extracts short reads that might contain virus integration information for further analysis. The reads whose one ends were mapped to the human genome and other ends were mapped to the virus genome are clustered to get the candidate integration regions (bottom right). The reads that are soft-clippedly mapped to the human or the virus genome are realigned to candidate regions to get the exact breakpoints (bottom left). The soft-clipped parts of the short reads are marked with X’s