Hydra 0.5.3 / Hydra-Multi
Hydra detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments.
Hydra-Multi is a paired-end read structural variant discovery tool that is capable of integrating signals from hundreds of samples.
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Population-based structural variation discovery with Hydra-Multi.
Lindberg MR, Hall IM, Quinlan AR.
Bioinformatics. 2014 Dec 2. pii: btu771.
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Aaron R. Quinlan1, Royden A. Clark1, Svetlana Sokolova1, Mitchell L. Leibowitz1, Yujun Zhang2, Matthew E. Hurles2, Joshua C. Mell3 and Ira M. Hall
Genome Res. 2010. 20: 623-635