TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads

takeabreak

Version	Tool Shed	Owner	Galaxy instances where the tool is available
1.1.2+galaxy0	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org
1.1.2	toolshed.g2.bx.psu.edu	iuc	bipaa-galaxy.genouest.org
1.1.2	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org