ViralFusionSeq [VFS] download

VFS was fullly tested under Ubuntu/Debian system.

** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download

As of 2016, VFS is the only viral integration tool available at NIH HPC system.
https://hpc.nih.gov/apps/ViralFusionSeq/

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

VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events.

A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints.

Minimal user defined parameters are required.

Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section.

Citation: http://www.ncbi.nlm.nih.gov/pubmed/

Features

Applicable and fully tested using RNA-Seq and DNA-Seq data
Utilize both clipped-sequence (CS) and paired-end (RP) information to discover viral integration
Re-construction of fusion transcript sequence using CS and RP information

Project Samples

Project Activity

See All Activity >

License

GNU General Public License version 3.0 (GPLv3)

Follow ViralFusionSeq [VFS]

ViralFusionSeq [VFS] Web Site

Other Useful Business Software

MongoDB Atlas runs apps anywhere

Deploy in 115+ regions with the modern database for every enterprise.

MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.

Start Free

Rate This Project

User Ratings

5.0 out of 5 stars

★★★★★

★★★★

★★★

★★

★

ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

User Reviews

Filter Reviews:

All

tfileme Posted 2013-05-23

Viralfusionseq works great.

1 user found this review helpful.

Additional Project Details

Operating Systems

Linux

Languages

English

Intended Audience

Science/Research

Programming Language

Perl

Related Categories

Perl Bio-Informatics Software

Registered

2012-08-06

Similar Business Software

MEGA

MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis...

See Software
Genome Analysis Toolkit (GATK)

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK...

See Software
Emedgene

Emedgene streamlines your tertiary analysis workflows for rare disease genomics and other germline research applications. Emedgene is designed to accelerate the time and certainty in user-defined variant interpretation, prioritization, curation, and research report generation. Enable greater...

See Software
Galaxy

Galaxy is an open source, web-based platform for data-intensive biomedical research. If you are new to Galaxy start here or consult our help resources. You can install your own Galaxy by following the tutorial and choosing from thousands of tools from the tool shed. This instance of Galaxy is...

See Software
Microsoft Genomics

Instead of managing your own data centers, take advantage of Microsoft's scale and experience in running exabyte-scale workloads. Because Microsoft Genomics is on Azure, you have the performance and scalability of a world-class supercomputing center, on demand in the cloud. Take advantage of a...

See Software
Illumina Connected Analytics

Store, archive, manage, and collaborate on multi-omic datasets. Illumina Connected Analytics is a secure genomic data platform to operationalize informatics and drive scientific insights. Easily import, build, and edit workflows with tools like CWL and Nextflow. Leverage DRAGEN bioinformatics...

See Software