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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 retroviral mutagenesis screens.

Source text:
(Hocum et al., 2015) VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. BMC Bioinformatics.

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ViFi / Viral Integration and Fusion Identification
Combines phylogenetic methods with reference-based read mapping to identify viral integrations from whole genome sequencing (WGS) data and human-virus fusion mRNA from RNA-seq data. ViFi is a program that utilizes a combination of reference-based alignment mapping and ensemble of Hidden Markov Models (eHMMs) to represent the viral families of interest to identify viral reads. Moreover, it incorporates mappability scores to reduce false positive detections.
Seeksv
Detects somatic structural variations (SVs) and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and the fragment with two ends unmapped. It can detect deletion, insertion, inversion and interchromosome transfer at single-nucleotide resolution. Unlike others methods, seeksv merges soft clipped-reads from the same breakpoint into a clipped long sequence individually and does not rely on any of the assembly software.
INSPIIRED / INtegration Site PIpeline for pairedend REaDs
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 biochemical method for integration site isolation, which achieves the critical criteria of suppressing PCR contamination between samples while sampling randomly from the pool of integrated DNAs. This tool accommodates analysis of integration in both single-copy and repeated sequences.
VISA / Vector Integration Site Analysis
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.
Ub-ISAP / UNIX-based vector Integration Site Analysis Pipeline
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 vector integration sites (ISs) from next-generation sequencing (NGS) data generated from genomic DNA (gDNA) (regardless of species origin) without the need to develop custom scripts. It was designed to analyze junction fragments generated from a range of custom library preparation methods including ligation-mediated polymerase chain reaction (LM-PCR) or Mu transposition based methods.
VISMapper
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 detailed view of the region in which the ISs occur and a threshold based on the number of reads that supports ISs, which also help in finding specific cancer genes or genes of specific cancer types. The software provides an interactive contextualized visualization of the results which can be furnished with genomic features including reads mapped and genes.
hiReadsProcessor
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 parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for quality control (QC) and abundance quantification. This software also offers functions to prepend name attribute of a list to DNAStringSet, to add a specific feature/attribute to the sampleInfo object and many others.
QuickMap
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').
HISAP / High-Througput Insertion Site Analysis Pipeline
Obsolete
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.
MAVRIC
Obsolete
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 comparison of data from different studies. Upload sequences to MAVRIC is possible by two ways: (1) input the text manually, (2) browse its own file containing FASTA formatted sequences. The user has to choose the quality thresholds and note which database versions and filtering options are used.
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