Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

VirusFinder | Software for detection of viruses and their integration sites in host genomes through NGS data

A software tool for characterizing intra-host viruses through next generation sequencing (NGS) data. It implements our recently developed algorithm, Virus intEgration site detection through Reference SEquence customization (VERSE) as well as other new features. Specifically, VirusFinder 2 detects virus infection, co-infection with multiple viruses, mutations in the virus genomes, in addition to virus integration sites in host genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 can not only work for the human genome data, but also other organisms with available reference genome sequences (e.g. animals). VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

VirusFinder forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

VirusFinder classification

  • Viruses

VirusFinder specifications

Unique identifier:
Command line interface
Input data:
Sequenced from a host, a reference host genome, and a reference virus genome.
Operating system:
Computer skills:
Software type:
Restrictions to use:
Input format:
Programming languages:
BASH, shell, Java

VirusFinder distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

VirusFinder support


This tool is not available anymore.


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA

Funding source(s)

Supported in part by National Institutes of Health grants (R01LM011177, P30CA68485, P50CA098131, and P50CA095103) and Ingram Professorship Funds.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.