ViralFusionSeq
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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, Gene structure, Sequence assembly (de novo assembly), Mapping |
| Principal bioinformatics method(s) | Read mapping, Read pre-processing, Sequence alignment, Sequence 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
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 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'.
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