quaqc: efficient and quick ATAC-seq quality control and filtering.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39475432.
- Also identified by DOI 10.1093/bioinformatics/btae649 and PMC identifier 11549019.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
"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. 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.
Medical subject headings
- Software
- Quality Control