Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, Bellaterra, Barcelona, 08193, Spain.
Bioinformatics. 2024 Nov 1;40(11). doi: 10.1093/bioinformatics/btae649.
"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.
"quaqc" 允许对 NGS 数据进行特定于 ATAC-seq 的质量控制和读取过滤，处理时间最短，内存开销极低。高效的扩展实现允许广泛的用例，从在个人笔记本电脑上处理单个样本到在计算集群上并行处理数千个样本。辅助 R 包 "quaqcr" 允许交互式程序执行和结果探索。
源代码和文档可从 https://github.com/bjmt/quaqc 和 https://github.com/bjmt/quaqcr 免费下载，遵循 GPLv3 许可证。"quaqc" 是用 C 语言编写的，已经在 macOS 和 Linux 上进行了测试。辅助 "quaqcr" 包仅需要 R 编程语言。与本文档相关的程序和代码的固定版本可在 https://zenodo.org/records/13833437 找到。
