BreakDancer, released under GPLv3, is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.

Please read our paper for a detailed description of the algorithm.

Using BreakDancer

You can easily install a binary distribution of BreakDancer on your Ubuntu 8.04 or later system in a few moments using these simple installation instrutions.

Once the package is installed, please review the documentation for detailed instructions.

Getting Help

Please join the Breakdancer Mailing List, or peruse the archives to see if your question may have already been answered.

How to Cite

We appreciate your citing the Breakdancer paper published in Nature Methods if you make use of this tool or related methods.

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