VFS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VFS

Tool usage distribution map

This map represents all the scientific publications referring to VFS per scientific context
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Associated diseases

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VFS specifications


Unique identifier OMICS_00224
Name VFS
Alternative name ViralFusionSeq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Ting-Fung Chan

Publication for ViralFusionSeq

VFS citations


Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] roViDE, Readscan, Rega Typing Tool, RIEMS, RINS, SLIM, SURPI, Taxy-Pro, “Unknown pathogens from mixed clinical samples,” VIP and ViromeScan), or even days (5 workflows: Exhaustive Iterative Assembly, ViralFusionSeq, VirFind, VirusFinder and VirusSeq). […]


ChimericSeq: An open source, user friendly interface for analyzing NGS data to identify and characterize viral host chimeric sequences

PLoS One
PMCID: 5567911
PMID: 28829778
DOI: 10.1371/journal.pone.0182843

[…] ] can detect viral integration sites in whole-transcriptome sequencing (RNA-Seq) data, but focus on the human genome and a predefined selection of viral genomes. VirusSeq and another similar program, ViralFusionSeq [], both use alignment algorithms that require high CPU resources, thereby taking a significant amount of time to process whole genome sequencing (WGS) data. Although newer tools such a […]


Cis perturbation of cancer drivers by the HTLV 1/BLV proviruses is an early determinant of leukemogenesis

Nat Commun
PMCID: 5457497
PMID: 28534499
DOI: 10.1038/ncomms15264
call_split See protocol

[…] Mispaired and soft-clipped reads supporting virus–host hybrid transcripts were identified using a custom two-pass alignment scheme as described in ViralFusionSeq. RNA-seq paired-end reads were aligned to the host genome using BWA (default parameter except -k 19 and -L 1) and mispaired and soft-clipped reads (minimum 8 soft-clipped nts) were re-a […]


GENE IS: Time Efficient and Accurate Analysis of Viral Integration Events in Large Scale Gene Therapy Data

Mol Ther Nucleic Acids
PMCID: 5363413
PMID: 28325279
DOI: 10.1016/j.omtn.2016.12.001

[…] s admit a limited set of reference genomes, do not expose multi-threading, and have limits on the amount of input data. The targeted sequencing analysis tools available, however (i.e., Virus-Clip and ViralFusionSeq), have their primary focus on cancer genome data analysis. Also, the mechanism used to detect integration site is dissimilar from the objective of gene therapy safety studies, and it is […]


Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology

BMC Genomics
PMCID: 5094076
PMID: 27806689
DOI: 10.1186/s12864-016-3203-3

[…] ViralFusionSeq (VFS) [] was used, with default parameters, to identify any viral-human fusion transcripts in each of our sample RNA-Seq datasets. As with viral alignment by TopHat2 (described above), […]

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VFS institution(s)
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
VFS funding source(s)
Supported in part by a General Research Fund (GRF461708), a Theme-based Research Scheme (Ref. no. T12-403/11), the Research Grant Committee, and a fund (ITF UIM/216) from the Innovation and Technology Commission.

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