Does anyone know a tool to find double strand breaks from a read mapping? They cannot be simply found by coverage drops, because bases to the left and to the right from the break can be covered by quite a lot of reads. Double strand breaks can be found by the absence of reads that span the points of double strand breaks. The task seems to be obvious but I cannot find a tool which is capable of doing this. The sequencing technology is Oxford Nanopore.
I will be grateful for help