{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T15:10:10Z","timestamp":1759072210725,"version":"3.44.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T00:00:00Z","timestamp":1759017600000},"content-version":"vor","delay-in-days":28,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32000097"],"award-info":[{"award-number":["32000097"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFA0806200","2022YFC2009802","2021YFC2501800"],"award-info":[{"award-number":["2022YFA0806200","2022YFC2009802","2021YFC2501800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transposase enzyme linked long-read sequencing (TELL-seq) technology generates barcode-linked reads, facilitating whole-genome sequencing (WGS), and complete assembly with improved accuracy and reduced costs. Unlike mate-pair sequencing technology, TELL-seq employs a near-full-sequence tagging strategy that allows more efficient capture of comprehensive genomic information. However, assembly algorithms and software capable of fully leveraging the characteristics of TELL-seq technology to effectively assemble genomic sequences at the megabase-scale are lacking, particularly for bacteria and their plasmids. In this study, we present TELL-seq barcode-assisted scaffold assembler (TELLBASE), a de novo genome assembler designed specifically for assembling bacterial genomes using TELL-seq-derived linked reads. In assembly tests involving bacteria such as Acinetobacter baumannii, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Staphylococcus aureus, TELLBASE exhibited exceptional efficacy in producing chromosome-level bacterial genomic sequences and successful identification of plasmids present in the sequenced strains. Comparative analysis revealed that TELLBASE significantly outperforms existing assemblers tailored for TELL-seq-derived linked reads, such as TuringAssembler and Ariadne, in terms of the completeness and accuracy of the assembled genomes. Therefore, TELLBASE shows promising potential for refining draft bacterial genomes and further applications in related fields. The package for TELLBASE is freely available on GitHub (https:\/\/github.com\/sosie1\/TELLBASE).<\/jats:p>","DOI":"10.1093\/bib\/bbaf504","type":"journal-article","created":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T14:33:55Z","timestamp":1759070035000},"source":"Crossref","is-referenced-by-count":0,"title":["TELLBASE: a novel tool of TELL-seq barcode-assisted scaffold assembler for bacterial genomes"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-8746-5024","authenticated-orcid":false,"given":"Yutong","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University , No. 2005 Songhu Road, Yangpu district, Shanghai 200433 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianlong","family":"Kuang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan 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Changjiang Road, Xinwu district, Wuxi 214013 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenxian","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Wuxi Universal Sequencing Co., Ltd. , No. 35 South Changjiang Road, Xinwu district, Wuxi 214013 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Chen","sequence":"additional","affiliation":[{"name":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Yangpu district, Shanghai 200433 ,","place":["China"]},{"name":"Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University , No. 12 Wulumuqi Zhong Road, Jingan district, Shanghai 200040 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Wu","sequence":"additional","affiliation":[{"name":"Shanghai Sci-Tech Inno Center for Infection & Immunity 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