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Short description:
Please summarise the application in a few sentences. Avoid links here. SOAPfusion is a novel tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwards”. This enables the fusion discovery process to be more effective and sensitive, also with a specular performance under low coverage of sequencing far more better than other tools. http://soap.genomics.org.cn/SOAPfusion.html
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Transcriptomics, RNA-Seq, Gene structure,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina HiSeq, Illumina Solexa, 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 University of Hong Kong
== Description == <!-- Describe the application in the space below --> SOAPfusion is a novel tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwards”. This enables the fusion discovery process to be more effective and sensitive, also with a specular performance under low coverage of sequencing far more better than other tools. In the package, it encoporates several modules developped specifically for mapping RNA-seq reads, finding gene fusions and false positive elimination. One thing to note is that the SOAPfusion-aligner is designed for mapping RNA-seq reads both in an intact manner and segemental (with long distantance in-between, or on different chromosomes) manner, which can be applied in other bioinformatics senario requiring segmental mappings as well. SOAPfusion is accurate and efficient for fusion discovery under various sequencing coverage (10X~50X, see Section “Performance”) with high sensitivity (≥97%), low false positive rate (≤1.36%) and has a saturation level of 10X, highlighting its ability to detect fusions efficiently at low sequencing cost. The alogrithms and software in this package were developed by the Algorithm and Bioinformatics Group at The University of Hong Kong (Jikun Wu , Dr. S.M. Yiu). In collaboration with BGI (Zhiyu Peng, Wenqian Zhang). <!-- -->
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