Difference between revisions of "ViralFusionSeq"
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Contact authors at [http://seqanswers.com/wiki/User:Marcowanger SEQanswers] | 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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Revision as of 06:07, 4 December 2012
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Application data |
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| Created by | Jing-Woei Li, Raymond Wan |
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| Biological application domain(s) | Genomics, Fusion genes, Fusion transcripts, Viral genomics |
| Principal bioinformatics method(s) | Read Alignment, Read mapping, Read pre-processing, Split-read, de-novo assembly, targeted de novo assembly, Alignment, Assembly |
| Technology | Illumina |
| Created at | The Chinese University of Hong Kong |
| Maintained? | Yes |
| Input format(s) | Single-end and Paired end, FASTQ, (Compressed) FASTQ |
| Output format(s) | Custom, .fasta, FASTA |
| Software features | Accurately discover viral integration events and fusion transcripts |
| Programming language(s) | Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux |
Summary: Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly
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Description
Viral FusionSeq (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 VirusSeq is available at "Files" and "Blog" in sourceforge,respectively
Contact authors at SEQanswers ViralFusionSeq was developed at Hong Kong Bioinformatics Centre
Links
- ViralFusionSeq Homepage [ edit link ]
- ViralFusionSeq HOWTO [ edit link ]
- ViralFusionSeq Manual [ edit link ]
- ViralFusionSeq Source code [ edit link ]
- ViralFusionSeq Publication full text [ edit link ]
- ViralFusionSeq Publication full text [ edit link ]
References
To add a reference for ViralFusionSeq, enter the PubMed ID in the field below and click 'Add'.
Search for "ViralFusionSeq" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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