Abstract
BackgroundThe analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function.ResultsWe have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic.ConclusionUb-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/.
Highlights
ResultsWe have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIXbased workflow for automated integration site identification and annotation of both single and paired-end sequencing reads
The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy
UNIX-based vector integration site analysis pipeline (Ub-ISAP) provides researchers with a consistent methodology for the extraction of vector Integration site (IS) from next-generation sequencing (NGS) data generated from genomic DNA (gDNA) without the need to develop custom scripts
Summary
We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIXbased workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are classified as transcription start site-proximal, intragenic or intergenic
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