quaqcr: Quick ATAC-Seq QC

A wrapper around the 'quaqc' program described in Tremblay and Questa (2024) <doi:10.1093/bioinformatics/btae649>. 'quaqc' allows for assay for transposase-accessible chromatin using sequencing (ATAC-seq) specific quality control and read filtering of next-generation sequencing (NGS) data with minimal processing time and extremely low memory overhead. Any number of samples can be processed, using multiple threads if desired. 'quaqc' outputs a comprehensive set of aligned read metrics, including alignment size, fragment size, percent duplicates, mapq scores, read depth, GC content, and others. Although designed for ATAC-seq data, 'quaqc' can also be used for other unspliced DNA sequencing experiments (such as chromatin immunoprecipitation sequencing, or ChIP-seq) as many of the metrics are related to general sequencing quality. This R package also provides additional utilities for custom analyses and plotting of 'quaqc' results.

Version:	1.0.4
Depends:	R (≥ 3.6.0)
Imports:	methods, utils, jsonlite
Suggests:	testthat (≥ 3.0.0)
Published:	2026-05-19
DOI:	10.32614/CRAN.package.quaqcr (may not be active yet)
Author:	Benjamin Jean-Marie Tremblay [aut, cre]
Maintainer:	Benjamin Jean-Marie Tremblay <benjmtremblay at gmail.com>
BugReports:	https://github.com/bjmt/quaqcr/issues
License:	GPL (≥ 3)
URL:	https://github.com/bjmt/quaqcr
NeedsCompilation:	no
SystemRequirements:	quaqc (https://github.com/bjmt/quaqc)
Citation:	quaqcr citation info
Materials:	README, NEWS
CRAN checks:	quaqcr results

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