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.
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=quaqcr
to link to this page.
[aut, cre]