Quagga is a lightweight tool that calls architectural stripes from a 3C chromatin contact frequency matrix. (A) The workflow of Quagga. (B) A 3C family-type contact frequency matrix via a COOL or HIC file is processed into a horizontally or vertically loaded matrix, and a naive peak-finding algorithm is used; stripe indices and width are calculated based on the vertically or horizontally averaged row or column sums. (C) Significance testing is applied to the candidate stripes from the previous step. Called region windows are used to determine the appropriate length of the stripe and whether the stripe is enriched over the local background.