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Retroviral vector integration site detection software tools | Whole-genome sequencing data analysis

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for…
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Virus-Clip
Desktop

Virus-Clip

Detects viral integration. Virus Clip first exploits the alignment to virus…

Detects viral integration. Virus Clip first exploits the alignment to virus genome, then it extracts soft-clipped reads from the alignment and their associated soft clipped portions. Next, the…

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INSPIIRED
Desktop

INSPIIRED INtegration Site PIpeline for pairedend REaDs

Allows to work about viral integration sites and the longitudinal outcomes of…

Allows to work about viral integration sites and the longitudinal outcomes of gene therapy patients. INSPIIRED serves for quantitative analysis of integration site distributions. This is a…

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HPVDetector
Desktop

HPVDetector

Determines HPV types from next-generation sequence data without any…

Determines HPV types from next-generation sequence data without any prerequisite knowledge about virus types. HPVDetector is made of two running options: (i) the quick detects mode which detect HPV…

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VISMapper
Desktop

VISMapper

Allows users to detect consequences and potential risks of the viral vectors…

Allows users to detect consequences and potential risks of the viral vectors inserted in genomes. VISMapper provides a general perspective of all the Insertion Site (IS)s along the chromosomes, a…

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Ub-ISAP
Desktop

Ub-ISAP UNIX-based vector Integration Site Analysis Pipeline

Enables automated integration site identification and annotation of single and…

Enables automated integration site identification and annotation of single and paired-end sequencing reads. Ub-ISAP is a time and memory pipeline which provides a methodology for the extraction of…

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SeqMap
Web

SeqMap

A tool for identifying viral integration sites from LAM-PCR and LM-PCR…

A tool for identifying viral integration sites from LAM-PCR and LM-PCR analysis. SeqMap will extract vector sequence data then search existing genome databases for matches to the unique sequences…

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MAVRIC
Web

MAVRIC

Returns detailed information on the genomic location of the integration sites…

Returns detailed information on the genomic location of the integration sites and gives an overview of viral integration patterns. MAVRIC produces annotations for reanalysis of historical datasets or…

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VISPA
Web

VISPA Vector Integration Site Parallel Analysis

A pipeline for automated integration site identification and annotation based…

A pipeline for automated integration site identification and annotation based on a distributed environment with a simple Galaxy web interface. VISPA was successfully used for the bioinformatics…

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VISA
Web

VISA Vector Integration Site Analysis

Analyzes next-generation sequencing data for retroviral vector integration…

Analyzes next-generation sequencing data for retroviral vector integration sites (RISs). Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized…

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hiReadsProcesso…
Desktop

hiReadsProcessor

Contains set of functions which allow users to process ligation-mediated…

Contains set of functions which allow users to process ligation-mediated polymerase chain reaction (LM-PCR) products sequenced using any platform. hiReadsProcessor gives an excel/txt file containing…

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HISAP
Web

HISAP High-Througput Insertion Site Analysis Pipeline

Annotates viral vector insertion site information for a collection of samples.…

Annotates viral vector insertion site information for a collection of samples. HISAP was generated to characterize insertions sites of viral gene therapy vectors, previously amplified with…

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VirusFinder
Desktop

VirusFinder

A software tool for characterizing intra-host viruses through next generation…

A software tool for characterizing intra-host viruses through next generation sequencing (NGS) data. It implements our recently developed algorithm, Virus intEgration site detection through Reference…

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QuickMap
Web

QuickMap

Uniformly maps and analyzes human and murine vector-flanking sequences within…

Uniformly maps and analyzes human and murine vector-flanking sequences within seconds. Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion…

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