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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.

Bioinformatics (Oxford, England)
|October 30, 2024
PubMed
Summary
This summary is machine-generated.

The "quaqc" tool provides efficient, low-memory quality control and read filtering for ATAC-seq next-generation sequencing (NGS) data. Its scalable design supports diverse applications, from single samples to large-scale parallel processing.

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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.