This is the Linux app named ViralFusionSeq [VFS] whose latest release can be downloaded as vfs-2016-08-17.r2.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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SCREENSHOTS:
ViralFusionSeq [VFS]
DESCRIPTION:
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
Audience
Science/Research
Programming Language
Perl
This is an application that can also be fetched from https://sourceforge.net/projects/viralfusionseq/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.