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