Benchmarking of three stripe callers, including Quagga, Zebra, and Stripenn, with Hi-C contact maps. (A) Quagga's stripe lengths lie mostly in the expected range compared with Stripenn or Zebra. (B) Stripe widths for Quagga are also the most varied. (C) Aggregated peak pileups using a 2 Mb window centered on the point of the main diagonal nearest the stripe's anchor, which demonstrates the high variability of the stripe length and width Quagga captures. (D) Scaled Quagga pileups along the entire stripe length show Quagga's variability and distribution of stripes; the beginning of the stripe is fixed to the start position, and half its length in either direction is captured as a context sequence. (E) Examples of stripes called by Quagga, Zebra, and Stripenn from GM12878 Hi-C.