quaqc: efficient and quick ATAC-seq quality control and filtering

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Next-generation sequencing (NGS) generates vast amounts of data requiring robust quality control.
• Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a key technique for studying genome accessibility.
• Efficient processing of ATAC-seq data is crucial for large-scale genomic studies.

Purpose of the Study:

• To introduce "quaqc", a novel tool for ATAC-seq specific quality control and read filtering.
• To provide a computationally efficient solution with minimal memory overhead.
• To enable flexible data processing across various computational environments.

Main Methods:

• "quaqc" is implemented in C for high performance.
• A companion R package, "quaqcr", facilitates interactive use and result exploration.
• The software is designed for scalability, supporting single-sample to cluster-based processing.

Main Results:

• "quaqc" achieves ATAC-seq specific quality control and read filtering.
• The tool operates with minimal processing time and extremely low memory requirements.
• Scalable implementation supports diverse use cases from personal laptops to compute clusters.

Conclusions:

• "quaqc" offers an efficient and resource-friendly solution for ATAC-seq data processing.
• The "quaqcr" package enhances usability through interactive analysis.
• The tool is freely available, promoting accessibility in genomic research.