» A Bioconductor package for quality assessment of ATAC-seq data

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. ATACseqQC package is for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ (2018). “ATACseqQC: A Bioconductor package for post-alignment quality assessment of ATAC-seq data.” BMC Genomics, 19(1), 169. ISSN 1471-2164, doi: 10.1186/s12864-018-4559-3, https://doi.org/10.1186/s12864-018-4559-3.