{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T04:37:36Z","timestamp":1772080656705,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T00:00:00Z","timestamp":1742169600000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200200"],"award-info":[{"award-number":["2021YFF1200200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The encoded large DNA can be cloned and stored in vivo, capable of write-once and stable replication for multiple retrievals, offering potential in economic data archiving. Nanopore sequencing is advantageous in data access of large DNA due to its rapidity and long-read sequencing capability. However, the data readout is commonly limited by insertion and deletion (indel) errors and sequence assembly complexity. Here, a pragmatic soft-decision data readout is presented, achieving assembly-free sequence reconstruction, indel error correction, and ultra-low coverage data readout. Specifically, the watermark is cleverly embedded within large DNA fragments, allowing for the direct localization of raw reads via watermark alignment to avoid complex read assembly. A soft-decision forward\u2013backward algorithm is proposed, which can identify indel errors and provide probability information to the error correction code, enabling error-free data recovery. Additionally, a minimum state transition is maintained, and a read segmentation is incorporated to achieve fast information reading. The readout assays for two circular plasmids (~51\u00a0kb) with different coding rates were demonstrated and achieved error-free recovery directly from noisy reads (error rate\u2009~1%) at coverage of 1\u20134\u00d7. Simulations conducted on large-scale datasets across various error rates further confirm the scalability of the method and its robust performance under extreme conditions. This readout method enables nearly single-molecule recovery of large DNA, particularly suitable for rapid readout of DNA storage.<\/jats:p>","DOI":"10.1093\/bib\/bbaf102","type":"journal-article","created":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T03:36:21Z","timestamp":1742182581000},"source":"Crossref","is-referenced-by-count":5,"title":["Pragmatic soft-decision data readout of encoded large DNA"],"prefix":"10.1093","volume":"26","author":[{"given":"Qi","family":"Ge","sequence":"first","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]},{"given":"Rui","family":"Qin","sequence":"additional","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]},{"given":"Shuang","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]},{"given":"Quan","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]},{"given":"Changcai","family":"Han","sequence":"additional","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]},{"name":"Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology , School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4880-8186","authenticated-orcid":false,"given":"Weigang","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Microelectronics, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]},{"name":"Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology , School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]},{"name":"Frontier Science Center for Synthetic Biology , Ministry of Education, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,17]]},"reference":[{"key":"2025031703360034600_ref1","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/s41576-019-0125-3","article-title":"Molecular digital data storage using DNA","volume":"20","author":"Ceze","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2025031703360034600_ref2","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1126\/science.1226355","article-title":"Next-generation digital information storage in 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