ViralFusionSeq [VFS] Icon

ViralFusionSeq [VFS]

beta

Accurately discover viral integration events and fusion transcripts

5.0 Stars (4)
3 Downloads (This Week)
Last Update:
Download vfs-2014-01-06-r1288.tar.gz
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Description

VFS was fullly tested under Ubuntu/Debian system. I suggest users to use VFS in Debian system.

** Announcement 1**: Improved VFS coming soon.

** Announcement 2**: VFS is officially described in Bioinformatics

** Announcement 3 **: 1 minute crash course of VFS now available in sourceforge's "Wiki" section

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.

PubMed: http://www.ncbi.nlm.nih.gov/pubmed/23314

ViralFusionSeq [VFS] Web Site

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

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User Reviews

  • tfileme
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Viralfusionseq works great.

    Posted 05/23/2013
  • elliotking
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Simple to use.

    Posted 02/13/2013
  • danmartinez
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Runs smoothly

    Posted 01/24/2013
  • ryanfong
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Great app

    Posted 12/24/2012
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Additional Project Details

Languages

English

Intended Audience

Science/Research

Programming Language

Perl

Registered

2012-08-06
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