Related Experiment Video
Updated: Jun 9, 2025
ATAC-Seq Optimization for Cancer Epigenetics Research
Published on: June 30, 2022
quaqc: efficient and quick ATAC-seq quality control and filtering
Benjamin J M Tremblay1, Julia I Qüesta1
1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, Bellaterra, Barcelona, 08193, Spain.
Summary:
"quaqc" allows for ATAC-seq-specific quality control and read filtering of NGS data with minimal processing time and extremely low memory overhead. An efficient scaling implementation allows for a wide range of use cases, from processing individual samples processed on personal laptops to handling thousands of samples processed in parallel on compute clusters. The helper R package "quaqcr" allows for interactive program execution and exploration of results.
Availability And Implementation:
Source code and documentation are freely available for download from https://github.com/bjmt/quaqc and https://github.com/bjmt/quaqcr under the GPLv3 license. "quaqc" is implemented in C and has been tested on both macOS and Linux. The "quaqcr" helper package only requires the R programming language. Fixed versions of the programs and code associated with this manuscript can be found at https://zenodo.org/records/13833437.
