DOI: 10.1101/474445Nov 20, 2018Paper

TSD: A computational tool to study the complex structural variants using PacBio targeted sequencing data

BioRxiv : the Preprint Server for Biology
Guofeng MengGregory Fanning

Abstract

The PacBio sequencing is a powerful approach to study the DNA or RNA sequences in a longer scope. It is especially useful in exploring the complex structural variants generated by random integration or multiple rearrangements of internal or external sequences. However, there is still no tool designed to uncover their structural organization in the host genome. Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data. It allows researchers to identify and visualize the genomic structures of targeted sequences by unlimited splitting, alignment and assembly of long PacBio reads. Application to the sequencing data derived from an HBV integrated human cell line(PLC/PRF/5) indicated that TSD could recover the full profile of HBV integration events, especially for the regions with the complex human-HBV genome integrations and multiple HBV rearrangements. Compared to other long read analysis tools, TSD showed a better performance for detecting complex genomic structural variants. TSD is publicly available at: https://github.com/menggf/tsd .

Related Concepts

DNA
Gene Rearrangement
Genome
Genome, Human
Hepatitis B Virus
Morphogenesis
Research Personnel
RNA
Computer Software
Tay-Sachs Disease

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