Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Source text: Li et al., 2013.

G T A T C G C T A PathSeq PathSeq

PathSeq

A computational tool for the identification and analysis of microbial sequences…

A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable…

Desktop app
G T A T C G C T A VirusSeq VirusSeq

VirusSeq

An algorithmic tool for detecting known viruses and their integration sites…

An algorithmic tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. It takes FASTQ files (paired-end reads) as input.

Desktop app
G T A T C G C T A Viral Recombination… Viral Recombination Mapper

ViReMa Viral Recombination Mapper

Detects and reports recombination or fusion events in virus genomes using deep…

Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Desktop app
G T A T C G C T A Rapid Identification… Rapid Identification of Non-human Sequences

RINS Rapid Identification of Non-human Sequences

An intersection-based pathogen detection workflow that utilizes a user-provided…

An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. RINS is optimized…

Desktop app
G T A T C G C T A ViralFusionSeq ViralFusionSeq

VFS ViralFusionSeq

A versatile high-throughput sequencing (HTS) tool for discovering viral…

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution.

Desktop app
G T A T C G C T A READSCAN READSCAN

READSCAN

A highly scalable parallel program to identify non-host sequences (of potential…

A highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately…

Desktop app
G T A T C G C T A HIVCD HIVCD

HIVCD

An informatics tool developed to identify patient sequences that are too…

An informatics tool developed to identify patient sequences that are too similar to happen by chance alone.

Desktop app
G T A T C G C T A Recombination… Recombination Detection Program version 4

RDP4 Recombination Detection Program version 4

A Windows computer program that implements an extensive array of methods for…

A Windows computer program that implements an extensive array of methods for detecting and visualizing recombination in, and stripping evidence of recombination from, virus genome sequence…

Desktop app
G T A T C G C T A viGEN viGEN

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

Desktop app
G T A T C G C T A Tool for… Tool for RECombinations

T-RECs Tool for RECombinations

Employs pairwise alignment of sliding windows and can perform (i) genotyping,…

Employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv)…

Desktop app
G T A T C G C T A Pavian Pavian

Pavian

A web application for exploring metagenomics classification results, with a…

A web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pavian allows researchers to analyze, display and transform results from the…

Desktop app
G T A T C G C T A Seeksv Seeksv

Seeksv

An accurate tool for detecting somatic structural variations (SVs) and viral…

An accurate tool for detecting somatic structural variations (SVs) and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and…

Desktop app
G T A T C G C T A Virus Identification… Virus Identification Pipeline

VIP Virus Identification Pipeline

A one-touch computational pipeline for virus identification and discovery from…

A one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related…

Web app
G T A T C G C T A Metavisitor Metavisitor

Metavisitor

A free and open source set of Galaxy tools and workflows allowing both de novo…

A free and open source set of Galaxy tools and workflows allowing both de novo reconstruction of novel viruses and detection of already identified viral species from sequencing datasets. Using the…

Desktop app
G T A T C G C T A QQ-SNV QQ-SNV

QQ-SNV

A logistic regression classifier model developed for the Illumina sequencing…

A logistic regression classifier model developed for the Illumina sequencing platforms that uses the quantiles of the quality scores, to distinguish true single nucleotide variants from sequencing…

Desktop app
G T A T C G C T A Read Assignment… Read Assignment Method Based On K-mers

RAMBO-K Read Assignment Method Based On K-mers

Allows rapid and sensitive removal of unwanted host sequences from Next…

Allows rapid and sensitive removal of unwanted host sequences from Next Generation Sequencing (NGS) datasets. RAMBO-K shows a consistently high sensitivity and specificity across different datasets.…

Desktop app
G T A T C G C T A gCUP gCUP

gCUP

A computional coreceptor usage prediction model. gCUP is based on our recently…

A computional coreceptor usage prediction model. gCUP is based on our recently developed method T-CUP, but was redeveloped, parallelized and optimized for the use on graphics processing units (GPUs).…

Web app
G T A T C G C T A Enhanced… Enhanced Lowest-common-ancestor based Method

ELM Enhanced Lowest-common-ancestor based Method

An enhanced lowest-common-ancestor based method (ELM) to effectively identify…

An enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data.

Desktop app
G T A T C G C T A SearchSmallRNA SearchSmallRNA

SearchSmallRNA

A mapping package with a graphical interface to the assemblage of viral genomes…

A mapping package with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA presents the data graphically and shows statistical analyses…

Desktop app
G T A T C G C T A VirusHunter VirusHunter

VirusHunter

A fully automated and modular software package designed for mining sequence…

A fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin. It has been implemented in PERL.

Desktop app
G T A T C G C T A VirusFinder VirusFinder

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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