  Double-strand breaks (DSBs) in DNA are naturally occurring destructive events
in all organisms that may lead to genome instability. Cells employ various
repair methods known as non-homologous end joining (NHEJ), microhomology
mediated end joining (MMEJ), and homology-directed recombination (HDR). These
repair processes may lead to DNA sequence variations (e.g., nucleotide
insertions, deletions, and substitutions) at the location of the break.
Studying DNA DSB repair processes often involves the use of high throughput
sequencing assays to precisely quantify the sequence variations near the break
with software tools. Often methods of assessing and visualizing these data have
not taken into account the full complexity of the sequencing data, such as the
frequency, type, and position of the sequence variations in a single
comprehensive representation. Here we present a method that allows
visualization of the overall variation pattern as well as comparison of these
patterns among experimental setups.
