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VFS specifications

Information


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

Versioning


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Maintainer


  • person_outline Ting-Fung Chan <>

Publication for ViralFusionSeq

VFS in pipeline

2017
PMCID: 5457497
PMID: 28534499
DOI: 10.1038/ncomms15264

[…] deletion from hts-based integration mapping data., 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) […]


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VFS in publications

 (2)
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] 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)., for 17 workflows for which these data were available, we looked for correlations by plotting performance scores against the analysis steps […]

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

[…] multiple softwares for detecting pathogen sequences in host sequence data have become available [, –]. here, to identify the viral-human fusion transcripts expressed in our epithelia, we used the viralfusionseq (vfs) software [, ]. vfs was chosen over alternatives due to its optimization for rna-seq data from the illumina platform, the ability to define our own reference virus genome, as well […]


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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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