SOAPfusion
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Application data |
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| Created by | T. W. Lam |
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| Biological application domain(s) | Transcriptomics, RNA-Seq, Gene structure |
| Technology | Illumina HiSeq, Illumina Solexa, Illumina |
| Created at | The University of Hong Kong |
| Maintained? | Yes |
| Input format(s) | FASTQ |
| Output format(s) | Delimited Text |
| Software features | finding fusions directly and verifying them |
| Programming language(s) | Perl, C++ |
| Operating system(s) | Linux 64 |
| Contact: | soap@genomics.org.cn |
Summary: 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 200px|right
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Description
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).
Links
References
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