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)…
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PathSeq
Cloud

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…

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IMSA
Desktop

IMSA Integrated Metagenomic Sequence Analysis

Meets the above criteria and is available for public use. IMSA is a system for…

Meets the above criteria and is available for public use. IMSA is a system for Integrated Metagenomic Sequence Analysis of high throughput sequence data. It can be used to analyze data from genomic…

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RDP4
Desktop

RDP4 Recombination Detection Program

Implements an extensive array of methods for detecting and visualizing…

Implements an extensive array of methods for detecting and visualizing recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP is capable of analyzing…

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ViReMa
Desktop

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.

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Seeksv
Desktop

Seeksv

Detects somatic structural variations (SVs) and viral integration events.…

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…

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RINS
Desktop

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…

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VirusSeq
Desktop

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.

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PathoScope
Desktop

PathoScope

Performs all necessary computational analysis steps; including reference genome…

Performs all necessary computational analysis steps; including reference genome library extraction and indexing, read quality control and alignment, strain identification, and summarization and…

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VFS
Desktop

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.

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READSCAN
Desktop

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…

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VirusSeeker
Desktop

VirusSeeker

Uses for mining sequence data to identify sequences of viral origin.…

Uses for mining sequence data to identify sequences of viral origin. VirusSeeker is a set of fully automated and modular software package optimized for analysis of data generated by the Illumina next…

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T-RECs
Desktop

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)…

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Metavisitor
Web

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…

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BatVI
Desktop

BatVI

Predicts viral integrations. BatVI identifies a set of probable chimeric reads…

Predicts viral integrations. BatVI identifies a set of probable chimeric reads using the sensitive BLAST aligner. It can detect viral integrations having very low coverage. For detecting viral…

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viGEN
Desktop

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…

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RAMBO-K
Desktop

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.…

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Pavian
Desktop

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…

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VIP
Desktop

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…

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gCUP
Desktop

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).…

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HIVCD
Desktop

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.

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QQ-SNV
Desktop

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…

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VirFind
Desktop

VirFind

Maps the reads to reference genomes. VirFind is a method specifically developed…

Maps the reads to reference genomes. VirFind is a method specifically developed for virus detection and discovery able to: (i) map and filter out host reads, (ii) deliver files of virus reads with…

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ELM
Web

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.

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SearchSmallRNA
Desktop

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…

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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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VirusHunter
Desktop

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.

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