Record added by Jurg Ott (the original Rockefeller list)
BreakDancer 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.
http://gmt.genome.wustl.edu/breakdancer/current/
Perl, C++
Chen, Wallis, McLellan, Larson, Kalicki, Pohl, McGrath, Wendl, Zhang, Locke, Shi, Fulton, Ley, Wilson, Ding, Mardis (2009), “BreakDancer: an algorithm for high-resolution mapping of genomic structural variation”, Nature Methods, 6:677-681.