{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:15Z","timestamp":1753875855078,"version":"3.41.2"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,10,30]],"date-time":"2024-10-30T00:00:00Z","timestamp":1730246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["MCIN\/AEI\/10.13039\/501100011033"],"award-info":[{"award-number":["MCIN\/AEI\/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>\u201cquaqc\u201d 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 \u201cquaqcr\u201d allows for interactive program execution and exploration of results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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. \u201cquaqc\u201d is implemented in C and has been tested on both macOS and Linux. The \u201cquaqcr\u201d 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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae649","type":"journal-article","created":{"date-parts":[[2024,10,30]],"date-time":"2024-10-30T17:29:49Z","timestamp":1730309389000},"source":"Crossref","is-referenced-by-count":0,"title":["quaqc: efficient and quick ATAC-seq quality control and filtering"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7441-2951","authenticated-orcid":false,"given":"Benjamin J M","family":"Tremblay","sequence":"first","affiliation":[{"name":"Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB , Bellaterra, Barcelona, 08193,","place":["Spain"]}]},{"given":"Julia I","family":"Q\u00fcesta","sequence":"additional","affiliation":[{"name":"Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB , Bellaterra, Barcelona, 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