{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T21:45:16Z","timestamp":1782855916334,"version":"3.54.5"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T00:00:00Z","timestamp":1772064000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"AMD. SAFARI Research Group"},{"name":"Google, Intel, Microsoft, VMware"},{"name":"Semiconductor Research Corporation (SRC), the European Union\u2019s Horizon","award":["101047160"],"award-info":[{"award-number":["101047160"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"crossref","award":["200021_213084"],"award-info":[{"award-number":["200021_213084"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Max Planck ETH Center for Learning Systems and by SNSF","award":["#200550"],"award-info":[{"award-number":["#200550"]}]},{"DOI":"10.13039\/501100001711","name":"SNSF","doi-asserted-by":"publisher","award":["#200550"],"award-info":[{"award-number":["#200550"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e. without basecalling). However, existing solutions cannot interpret raw signals directly if a reference genome is unknown due to a lack of accurate mechanisms to handle increased noise in pairwise raw signal comparison. Our goal is to enable the direct analysis of raw signals without a reference genome. To this end, we propose Rawsamble, the first mechanism that can identify regions of similarity between all raw signal pairs, known as all-vs-all overlapping, using a hash-based search mechanism.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We use these overlaps to construct de novo assembly graphs with an existing assembler, miniasm, off-the-shelf. To our knowledge, these are the first de novo assemblies ever constructed directly from raw signals without basecalling. Our extensive evaluations across multiple genomes of varying sizes show that Rawsamble provides a significant speedup (on average by 5.01\u00d7 and up to 23.10\u00d7) and reduces peak memory usage (on average by 5.74\u00d7 and up to by 22.00\u00d7) compared to a conventional genome assembly pipeline using the state-of-the-art tools for basecalling (Dorado\u2019s fastest mode) and overlapping (minimap2) on a CPU. We find that around one-third of Rawsamble\u2019s overlapping pairs are also found by minimap2. We find that when we use overlapping reads from Rawsamble, we can construct unitigs that are (i) as accurate as those built from minimap2\u2019s overlaps and (ii) up to half a chromosome in length (e.g. 2.3 million bases for E. coli).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Rawsamble is available at https:\/\/github.com\/CMU-SAFARI\/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag087","type":"journal-article","created":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T12:46:53Z","timestamp":1772023613000},"source":"Crossref","is-referenced-by-count":2,"title":["Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6548-7863","authenticated-orcid":false,"given":"Can","family":"Firtina","sequence":"first","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]},{"name":"Department of Computer Science, University of Maryland , MD 20742,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5731-484X","authenticated-orcid":false,"given":"Maximilian","family":"Mordig","sequence":"additional","affiliation":[{"name":"Department of Computer Science, ETH Zurich , Zurich, 8092,","place":["Switzerland"]},{"name":"Max Planck Institute for Intelligent Systems , Tubingen, 72076,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2125-6086","authenticated-orcid":false,"given":"Harun","family":"Mustafa","sequence":"additional","affiliation":[{"name":"Department of Computer Science, ETH Zurich , Zurich, 8092,","place":["Switzerland"]},{"name":"University Hospital Zurich , Zurich, 8091,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Zurich, 8057,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7519-524X","authenticated-orcid":false,"given":"Sayan","family":"Goswami","sequence":"additional","affiliation":[{"name":"Department of Computer Science, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0833-0042","authenticated-orcid":false,"given":"Nika","family":"Mansouri Ghiasi","sequence":"additional","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Mercogliano","sequence":"additional","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4503-6073","authenticated-orcid":false,"given":"Furkan","family":"Eris","sequence":"additional","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2581-8637","authenticated-orcid":false,"given":"Joel","family":"Lindegger","sequence":"additional","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3411-0692","authenticated-orcid":false,"given":"Andr\u00e9","family":"Kahles","sequence":"additional","affiliation":[{"name":"Department of Computer Science, ETH Zurich , Zurich, 8092,","place":["Switzerland"]},{"name":"University Hospital Zurich , Zurich, 8091,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Zurich, 8057,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0075-2312","authenticated-orcid":false,"given":"Onur","family":"Mutlu","sequence":"additional","affiliation":[{"name":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,26]]},"reference":[{"key":"2026031019335688800_btag087-B1","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s13059-026-03950-1","article-title":"Campolina: a deep neural framework for accurate segmentation of nanopore signals","volume":"27","author":"Baki\u0107","year":"2026","journal-title":"Genome Biol"},{"key":"2026031019335688800_btag087-B2","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1186\/s13059-021-02511-y","article-title":"SquiggleNet: real-time, direct classification of nanopore signals","volume":"22","author":"Bao","year":"2021","journal-title":"Genome Biol"},{"key":"2026031019335688800_btag087-B3","doi-asserted-by":"publisher","first-page":"6960","DOI":"10.1021\/nn3019943","article-title":"Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence","volume":"6","author":"Bhattacharya","year":"2012","journal-title":"ACS Nano"},{"key":"2026031019335688800_btag087-B4","doi-asserted-by":"crossref","first-page":"19656","DOI":"10.1038\/s41598-023-46771-z","article-title":"Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance","volume":"13","author":"Bloemen","year":"2023","journal-title":"Sci Rep"},{"key":"2026031019335688800_btag087-B5","doi-asserted-by":"crossref","first-page":"e0178751","DOI":"10.1371\/journal.pone.0178751","article-title":"DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads","volume":"12","author":"Bo\u017ea","year":"2017","journal-title":"PLoS One"},{"key":"2026031019335688800_btag087-B6","doi-asserted-by":"crossref","first-page":"4191","DOI":"10.1093\/bioinformatics\/btaa297","article-title":"DeepNano-blitz: a fast base caller for MinION nanopore sequencers","volume":"36","author":"Bo\u017ea","year":"2020","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B7","doi-asserted-by":"crossref","first-page":"1429306","DOI":"10.3389\/fgene.2024.1429306","article-title":"TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering","volume":"15","author":"Cavlak","year":"2024","journal-title":"Front Genet"},{"key":"2026031019335688800_btag087-B8","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/bioinformatics\/btw569","article-title":"Nanocall: an open source basecaller for oxford nanopore sequencing data","volume":"33","author":"David","year":"2017","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B9","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/nbt.3423","article-title":"Three decades of nanopore sequencing","volume":"34","author":"Deamer","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026031019335688800_btag087-B10","author":"Dunn","year":"2021"},{"key":"2026031019335688800_btag087-B11","doi-asserted-by":"crossref","first-page":"3215","DOI":"10.1093\/bioinformatics\/btw470","article-title":"LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads","volume":"32","author":"El-Metwally","year":"2016","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B12","doi-asserted-by":"publisher","DOI":"10.1145\/3765612.3767302","volume-title":"ACM-BCB","author":"Eris","year":"2025"},{"key":"2026031019335688800_btag087-B13","doi-asserted-by":"crossref","first-page":"i297","DOI":"10.1093\/bioinformatics\/btad272","article-title":"RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes","volume":"39","author":"Firtina","year":"2023","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B14","doi-asserted-by":"crossref","first-page":"lqad004","DOI":"10.1093\/nargab\/lqad004","article-title":"BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis","volume":"5","author":"Firtina","year":"2023","journal-title":"NAR Genom Bioinform"},{"key":"2026031019335688800_btag087-B15","doi-asserted-by":"crossref","first-page":"btae478","DOI":"10.1093\/bioinformatics\/btae478","article-title":"RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization","volume":"40","author":"Firtina","year":"2024","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B16","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1186\/s12859-020-03697-x","article-title":"GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis","volume":"21","author":"Gamaarachchi","year":"2020","journal-title":"BMC Bioinform"},{"key":"2026031019335688800_btag087-B17","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1109\/TCBB.2020.3039244","article-title":"SACall: a neural network basecaller for oxford nanopore sequencing data based on self-attention mechanism","volume":"19","author":"Huang","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2026031019335688800_btag087-B18","author":"Sovi\u0107","year":"2013"},{"key":"2026031019335688800_btag087-B19","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2026031019335688800_btag087-B20","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1021\/la803556p","article-title":"Controlling the translocation of single-stranded DNA through a-hemolysin ion channels using viscosity","volume":"25","author":"Kawano","year":"2009","journal-title":"Langmuir"},{"key":"2026031019335688800_btag087-B21","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026031019335688800_btag087-B22","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1093\/bioinformatics\/btaa953","article-title":"Halcyon: an accurate basecaller exploiting an encoder\u2013decoder model with monotonic attention","volume":"37","author":"Konishi","year":"2021","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B23","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41587-020-0731-9","article-title":"Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED","volume":"39","author":"Kovaka","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2026031019335688800_btag087-B24","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1038\/s41592-025-02631-4","article-title":"Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment","volume":"22","author":"Kovaka","year":"2025","journal-title":"Nat Methods"},{"key":"2026031019335688800_btag087-B25","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B26","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B27","doi-asserted-by":"crossref","first-page":"196855","DOI":"10.1109\/ACCESS.2024.3520669","article-title":"RawAlign: accurate, fast, and scalable raw nanopore signal mapping via combining seeding and alignment","volume":"12","author":"Lindegger","year":"2024","journal-title":"IEEE Access"},{"key":"2026031019335688800_btag087-B28","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nmeth.3444","article-title":"A complete bacterial genome assembled de novo using only nanopore sequencing data","volume":"12","author":"Loman","year":"2015","journal-title":"Nat Methods"},{"key":"2026031019335688800_btag087-B29","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/nmeth.3930","article-title":"Real-time selective sequencing using nanopore technology","volume":"13","author":"Loose","year":"2016","journal-title":"Nat Methods"},{"key":"2026031019335688800_btag087-B30","author":"Lv","year":"2020"},{"key":"2026031019335688800_btag087-B31","first-page":"1256","article-title":"Nanopore sequencing data analysis: state of the art, applications and challenges","volume":"19","author":"Magi","year":"2018","journal-title":"Brief Bioinform"},{"key":"2026031019335688800_btag087-B32","author":"Miculinic","year":"2019"},{"issue":"Suppl 2","key":"2026031019335688800_btag087-B33","doi-asserted-by":"crossref","first-page":"ii79","DOI":"10.1093\/bioinformatics\/bti1114","article-title":"The fragment assembly string graph","volume":"21","author":"Myers","year":"2005","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B34","doi-asserted-by":"crossref","first-page":"vbad017","DOI":"10.1093\/bioadv\/vbad017","article-title":"baseLess: lightweight detection of sequences in raw MinION data","volume":"3","author":"Noordijk","year":"2023","journal-title":"Bioinform Adv"},{"key":"2026031019335688800_btag087-B35","doi-asserted-by":"crossref","first-page":"4661","DOI":"10.1093\/bioinformatics\/btab528","article-title":"Nanopore base calling on the edge","volume":"37","author":"Pere\u0161\u00edni","year":"2021","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B36","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-0716-2996-3_1","volume-title":"Nanopore Sequencing: Methods and Protocols","author":"Pugh","year":"2023"},{"key":"2026031019335688800_btag087-B37","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1093\/bioinformatics\/btx471","article-title":"Faucet: streaming de novo assembly graph construction","volume":"34","author":"Rozov","year":"2018","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B38","doi-asserted-by":"crossref","first-page":"45","DOI":"10.26502\/acbr.50170318","article-title":"Rapid real-time squiggle classification for read until using RawMap","volume":"7","author":"Sadasivan","year":"2023","journal-title":"Arch Clin Biomed Res"},{"key":"2026031019335688800_btag087-B39","doi-asserted-by":"crossref","first-page":"137","DOI":"10.26502\/jbb.2642-91280134","article-title":"Accelerated dynamic time warping on GPU for selective nanopore sequencing","volume":"07","author":"Sadasivan","year":"2024","journal-title":"J Biotechnol Biomed"},{"key":"2026031019335688800_btag087-B40","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1109\/ICIAfS52090.2021.9606056","author":"Samarasinghe","year":"2021"},{"key":"2026031019335688800_btag087-B41","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1093\/bioinformatics\/btv046","article-title":"Analysis of nanopore data using hidden markov models","volume":"31","author":"Schreiber","year":"2015","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B42","author":"Scott","year":"2022"},{"key":"2026031019335688800_btag087-B43","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s12859-023-05151-0","article-title":"DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing","volume":"24","author":"Senanayake","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2026031019335688800_btag087-B44","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1093\/bib\/bby017","article-title":"Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions","volume":"20","author":"Senol Cali","year":"2019","journal-title":"Brief Bioinform"},{"key":"2026031019335688800_btag087-B45","doi-asserted-by":"crossref","first-page":"giad046","DOI":"10.1093\/gigascience\/giad046","article-title":"Efficient real-time selective genome sequencing on resource-constrained devices","volume":"12","author":"Shih","year":"2023","journal-title":"GigaScience"},{"key":"2026031019335688800_btag087-B46","doi-asserted-by":"crossref","first-page":"i287","DOI":"10.1093\/bioinformatics\/btae213","article-title":"Sigmoni: classification of nanopore signal with a compressed pangenome index","volume":"40","author":"Shivakumar","year":"2024","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B47","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res"},{"key":"2026031019335688800_btag087-B48","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s13059-024-03181-2","article-title":"RUBICON: a framework for designing efficient deep learning-based genomic basecallers","volume":"25","author":"Singh","year":"2024","journal-title":"Genome Biol"},{"key":"2026031019335688800_btag087-B49","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1073\/pnas.0705349105","article-title":"Noise in solid-state nanopores","volume":"105","author":"Smeets","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026031019335688800_btag087-B50","doi-asserted-by":"publisher","first-page":"giag005","DOI":"10.1093\/gigascience\/giag005","article-title":"Dynamont: a comprehensive cross-species comparison of ONT segmentation tools","author":"Spangenberg","year":"2026","journal-title":"GigaScience"},{"key":"2026031019335688800_btag087-B51","doi-asserted-by":"publisher","first-page":"giy037","DOI":"10.1093\/gigascience\/giy037","article-title":"Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning","volume":"7","author":"Teng","year":"2018","journal-title":"GigaScience"},{"key":"2026031019335688800_btag087-B52","doi-asserted-by":"crossref","first-page":"L37","DOI":"10.1016\/j.bpj.2012.04.009","article-title":"DNA base-calling from a nanopore using a Viterbi algorithm","volume":"102","author":"Timp","year":"2012","journal-title":"Biophys J"},{"key":"2026031019335688800_btag087-B53","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/s43588-021-00073-4","article-title":"Time- and memory-efficient genome assembly with Raven","volume":"1","author":"Vaser","year":"2021","journal-title":"Nat Comput Sci"},{"key":"2026031019335688800_btag087-B54","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B55","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1186\/s12859-023-05580-x","article-title":"Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden markov model and a residual LSTM network","volume":"24","author":"Xu","year":"2023","journal-title":"BMC Bioinform"},{"key":"2026031019335688800_btag087-B56","first-page":"100011","article-title":"Fast-bonito: a faster deep learning based basecaller for nanopore sequencing","volume":"1","author":"Xu","year":"2021","journal-title":"Artif Intell Life Sci"},{"key":"2026031019335688800_btag087-B57","doi-asserted-by":"publisher","first-page":"3877","DOI":"10.1093\/bioinformatics\/btac435","article-title":"MSRCall: a multi-scale deep neural network to basecall oxford nanopore sequences","volume":"38","author":"Yeh","year":"2022","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B58","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.3389\/fgene.2019.01332","article-title":"Causalcall: nanopore basecalling using a temporal convolutional network","volume":"10","author":"Zeng","year":"2019","journal-title":"Front Genet"},{"key":"2026031019335688800_btag087-B59","doi-asserted-by":"crossref","first-page":"i477","DOI":"10.1093\/bioinformatics\/btab264","article-title":"Real-time mapping of nanopore raw signals","volume":"37","author":"Zhang","year":"2021","journal-title":"Bioinformatics"},{"key":"2026031019335688800_btag087-B60","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1186\/s12859-020-3459-0","article-title":"Nanopore basecalling from a perspective of instance segmentation","volume":"21","author":"Zhang","year":"2020","journal-title":"BMC Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag087\/67136899\/btag087.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag087\/67136899\/btag087.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag087\/67136899\/btag087.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T23:34:11Z","timestamp":1773185651000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag087\/8499658"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,26]]},"references-count":60,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,2,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag087","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,3]]},"published":{"date-parts":[[2026,2,26]]},"article-number":"btag087"}}