Abstract
Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.Availability and Implementation: The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/.Contact: troyhawk@iupui.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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