Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility, due to its simplicity, speed, and low input material requirements. However, it can be difficult to evaluate data quality, particularly when processing many samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing ATAC-seq quality control results. We perform controlled ATAC-seq experiments and utilize ataqv to show that the ratio of Tn5 transposase to nuclei and sequencing flowcell cluster density induce reproducible technical bias in ATAC-seq results, significantly changing the fragment length distribution and enrichment of reads in promoter and enhancer chromatin states. ATAC-seq was performed using seven different concentrations of Tn5 transposase, on DNA isolated from GM12878 cells. In one experiment ('PCR-constant'), the same number of PCR cycles were used for each library and n = 6 different nuclear isolations were performed, resulting in 42 total libraries. In another experiment ('PCR-constant'), the number of PCR cycles for each library was selected via qPCR, n = 3 different nuclear isolations were performed (resulting in 21 separate libraries), and each library was sequenced one a sequencing run with low cluster density ('low') as well as on a run with high cluster density ('high')