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Short description:
Please summarise the application in a few sentences. Avoid links here. Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Genomics, Gene structure, Sequence assembly (de novo assembly), Mapping
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping, Read pre-processing, Sequence alignment, Sequence assembly,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
The Chinese University of Hong Kong
== Description == <!-- Describe the application in the space below --> 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 '''features comparison with [http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html VirusSeq]''' is available at "''[http://sourceforge.net/projects/viralfusionseq/files/ Files]''" and "''[http://sourceforge.net/p/viralfusionseq/blog/ Blog]''" in [http://sourceforge.net/projects/viralfusionseq/ sourceforge],respectively Contact authors at [http://seqanswers.com/wiki/User:Marcowanger SEQanswers] ViralFusionSeq was developed at [http://hkbic.cuhk.edu.hk/ Hong Kong Bioinformatics Centre] <!-- -->
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