Friday, September 17, 2010

hydra-sv - Project Hosting on Google Code

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.

It is important to note that Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster. In other words, it merely detects and reports breakpoints, but does not decide what type of SV (e.g. deletion, inversion, etc.) is indicated by the apparent breakpoint. This is an intentional decision, as we have observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. We suggest that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, we developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process.

Hydra was developed by Aaron Quinlan and Ira Hall at the University of Virginia. It is written in C++ and is under continued development. Therefore, please check back frequently, as we will continue to update the source code and documentation as Hydra and the methods leading up to it (e.g. aligners, alignment formats, sequence technologies and protocols) evolve.

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