{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T14:47:40Z","timestamp":1787237260742,"version":"build-2736575974"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T00:00:00Z","timestamp":1743984000000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian Research Council DECRA Fellowship","award":["DE230100178"],"award-info":[{"award-number":["DE230100178"]}]},{"name":"Australian Medical Research Futures Fund","award":["2016008"],"award-info":[{"award-number":["2016008"]}]},{"name":"Australian Medical Research Futures Fund","award":["2023126"],"award-info":[{"award-number":["2023126"]}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["2035037"],"award-info":[{"award-number":["2035037"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is running, reducing the turnaround time of the results. We introduce realfreq, a framework for obtaining real-time base modification frequencies while a nanopore sequencer is in operation. Realfreq calculates and allows access to the real-time base modification frequency results while the sequencer is running. We demonstrate that the data analysis rate with realfreq on a laptop computer can keep up with the output data rate of a nanopore MinION sequencer, while a desktop computer can keep up with a single PromethION 2 solo flowcell.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Realfreq is a free and open-source application implemented in C programming language and shell scripts. The source code and the documentation for realfreq can be found at https:\/\/github.com\/imsuneth\/realfreq. The version used for the manuscript is also available at https:\/\/doi.org\/10.5281\/zenodo.15128668.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf151","type":"journal-article","created":{"date-parts":[[2025,4,3]],"date-time":"2025-04-03T07:56:51Z","timestamp":1743667011000},"source":"Crossref","is-referenced-by-count":4,"title":["Realfreq: real-time base modification analysis for nanopore sequencing"],"prefix":"10.1093","volume":"41","author":[{"given":"Suneth","family":"Samarasinghe","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, UNSW Sydney , NSW 2052, Kensington,","place":["Australia"]},{"name":"Genomics and Inherited Disease Program, Garvan Institute of Medical Research , NSW 2010, Darlinghurst,","place":["Australia"]},{"name":"Centre for Population Genomics Garvan Institute of Medical Research and Murdoch Children\u2019s Research Institute , NSW 2010, 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