ASAP is a flexible analysis pipeline for ATAC-seq data analysis. Starting from raw ATAC-seq sequencing reads, ASAP outputs raw and filtered mapping files, coverage files (reads coverage ; tn5 insertion events coverage), fragment length distribution, read extraction based on fragment length, nucleosomes visualization and peak calling results. Overview of main steps Mapping Post-mapping processing and filtering: Filter (or not) reads that fall into user-defined blacklisted regions Select reads that do not carry more than minMismatch and filter by minimum mapping quality (MAPQ) Mark duplicated pairs Select concordant, non-duplicated pairs. Shift reads by 4bp as described in Schep et al.,2015: shift by 4bp toward to center of the transposition event. Compute read coverage Compute insertion events coverage Fragment length distribution Extract reads pairs based on a fragment length range and compute vizualisation arcs between fragment extremities (protection visualization) Peak calling: detection of accessible regions