{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T05:15:34Z","timestamp":1768194934445,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T00:00:00Z","timestamp":1749513600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korea Government","award":["2022M3C1A3090857"],"award-info":[{"award-number":["2022M3C1A3090857"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Error detection\/correction codes play an important role to reduce writing and\/or reading costs in DNA data storage. Sequence analysis algorithms also make a crucial effect on error correction but have been executed independently from the decoding of error correction codes. In conventional sequence analysis, low-quality reads are usually discarded. For DNA data storage, low-quality reads can be constructively used to sequence analysis with the assistance of error detection\/correction codes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We obtained the low-quality reads which failed to pass the chastity filter in Illumina NGS sequencing. We confirmed the effectiveness of the extra low-quality reads by providing error statistics and performing decoding with them. We proposed a sequence clustering algorithm for various-length reads and a consensus algorithm based on probabilistic majority and error detection to efficiently exploit the extra reads. The proposed methods reduced the reading cost by 6.83% on average and up to 19.67% while maintaining the writing cost.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/PParkJy\/SAD-DNAstorage (10.5281\/zenodo.15571858).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf335","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T18:36:07Z","timestamp":1749580567000},"source":"Crossref","is-referenced-by-count":2,"title":["Sequence analysis and decoding with extra low-quality reads for DNA data storage"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7146-334X","authenticated-orcid":false,"given":"Jiyeon","family":"Park","sequence":"first","affiliation":[{"name":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","place":["South Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ha Hyeon","family":"Jeon","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, POSTECH , Pohang 37673,","place":["South Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0705-0177","authenticated-orcid":false,"given":"Jeong Wook","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, POSTECH , Pohang 37673,","place":["South Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7854-7792","authenticated-orcid":false,"given":"Hosung","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","place":["South 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