ArticleBioinformatics (Oxford, England)2024
quaqc: efficient and quick ATAC-seq quality control and filtering.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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2 authors.
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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 programming language. Fixed versions of the programs and code associated with this manuscript can be found at https://zenodo.org/records/13833437.
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