MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
You can download the latest version of MultiBreakSV from GitHub.
MultiBreak-SV is described in the following publication:
A. Ritz, A. Bashir, S. Sindi, D. Hsu, I. Hajirasouliha, B. J. Raphael (2014). Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics. vol. 30 (24), pages 3458-3466. [Publisher Link]
MultiBreak-SV was also presented at the 2014 ISMB special interest group satellite conference HiTSeq: High Throughput Sequencing Algorithms & Applications in Boston, MA on July 12, 2014.