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 retroviral mutagenesis screens.
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 to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of RISs.
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 software maps the soft-clipped segments to the human reference genome, for finally affect human gene annotation. Besides, it makes possible to report the human and virus integration breakpoints to single-base resolution.
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 frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and Long Terminal Repeat (LTR) elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set').
Describes intra-host viruses through next generation sequencing (NGS) data. VirusFinder retrieves virus infection, co-infection with multiple viruses, mutations in the virus genomes, in addition to virus integration sites in host genomes. It reports novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. This tool deals with both paired-end and single-end data.
Assists users with the identification of integration site (IS). VISPA is a computational pipeline in which the sequence analysis for the integration site processing is compliant with paired-end reads. It includes a sequence quality filter before and after the alignment on the target genome. It also offers a classification and annotation module for integration sites.
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 (nr)LAM-PCR and sequenced with 454 pyrosequencing. Starting from raw 454 sequences HISAP trims vector and LAM-PCR specific sequence parts and aligns the remaining sequences to the host genome to obtain the integration sites. Information such as hit and nearby RefSeq genes, their distance and orientation to the integration site will be calculated automatically. The results are provided in an easy to use spreadsheet.
Maps viral integration events from next-generation sequencing (NGS) data. SC is an integration detection software that detects chimeras from paired or single end NGS reads then associate two chimeras that describe the integration event. This program reports chimera organism order, strand orientation and associates appropriate chimeras to infer the genetic content of viral integrations. It was assessed on a set of single-end IonTorrent reads from a purified Salmonella bacterium with an integrated bacteriophage.