Ataqv

ataqv is a toolkit for measuring and comparing ATAC-seq results and to make it easier to spot differences that might be caused by library prep or sequencing. The main program, ataqv, examines your aligned reads and reports some basic metrics, including:    reads mapped in proper pairs    optical or PCR duplicates    reads mapping to autosomal or mitochondrial references    the ratio of short to mononucleosomal fragment counts    mapping quality    various kinds of problematic alignments