ViralFusionSeq

Accurately discover viral integration events and fusion transcripts

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As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/

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.

Features

• Applicable and fully tested using RNA-Seq and DNA-Seq data
• Utilize both clipped-sequence (CS) and paired-end (RP) information to discover viral integration
• Re-construction of fusion transcript sequence using CS and RP information
• Minimal user defined parameters are required.
• Fully tested under Ubuntu/Debian system.

Installation

• Please refer to the manual VFS.manual.pdf

Run through docker

• Please check the scripts build_docker.sh and run_docker_example.sh to see how to build and run through docker

Citation

Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF. ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12. PMID: 23314323; PMCID: PMC3582262. https://pubmed.ncbi.nlm.nih.gov/23314323/

Announcements

• VFS is superior to Virus-Clip. Comparison report available here: https://github.com/TF-Chan-Lab/ViralFusionSeq/blob/master/VFS.vs.Virus-Clip.pdf
• VFS uses BLAST-2.2.26 which requires old version of database files, e.g. .nsd. These files can be created by BLAST-2.2.26 formatdb function (with "-o T" argument enabled) from FASTA sequences.
• Testing FASTQ files are available here: https://drive.google.com/drive/folders/1E0q0V3RXBuKfldS6kaOb_H4U9qxyn2mP?usp=sharing

Previous versions

• Please refer to the SourceForge for previous versions: https://sourceforge.net/projects/viralfusionseq/files/release/