Institute of Clinical
Molecular Biology

Kiel University
University Hospital

Schittenhelmstr. 12
24105 Kiel, Germany

Vy-PER | Virus integration detection bY Paired End Reads

Vy-PER is an open-source package of Linux command line tools for the highly sensitive and specific detection of virus integrations into a host genome from Illumina paired-end whole genome or whole transcriptome data.

Vy-PER was presented in a spotlight talk at the HiTSeq conference on 11 July 2014 (presentation | poster) and a manuscript published in Scientic Reports on 13 July 2015.


vyper v0.3 and examples (40KB)   hg19 and NCBI virus references (7.8GB)   release notes

Example data

L526401A (9.8 GB)   L526401A chr11 only (0.5 GB)   (from Chen et al, 2013).
198T (23 GB)   268T (24 GB)   (from Sung et al, 2012).
Please use 'wget url_of_file' from the linux command line.

Licence and disclaimer

Vy-PER is free for non-commercial use. No warranty whatsoever is given. See the README file and/or the comment lines in the header of in the vyper v0.3 download for how to implement the Vy-PER pipeline.

How to cite

Please cite this web page:
and also our manuscript:
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.
Forster M, Szymczak S, Ellinghaus D, Hemmrich G, Rühlemann M, Kraemer L, Mucha S, Wienbrandt L, Stanulla M; UFO Sequencing Consortium within I-BFM Study Group, Franke A.
Sci Rep. 2015 Jul 13;5:11534. doi: 10.1038/srep11534.


The development of Vy-PER was partly funded by: The German Office for Radiation Protection (BfS), The German Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (grant number 01ZX1306A, sysINFLAME); the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence 'Inflammation at Interfaces'; the EU Seventh Framework Programme [FP7/2007-2013, grant number 262055, ESGI].


Michael Forster and Silke Szymczak.

m [dott] forster [att] ikmb [dott] uni - kiel [dott] de
s [dott] szymczak [att] ikmb [dott] uni - kiel [dott] de