Quaqc: efficient and quick ATAC-seq quality control and filtering.

ABSTRACT:

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 pro

SUBMITTER: Tremblay BJM 

PROVIDER: S-EPMC11549019 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature