{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T11:56:01Z","timestamp":1787399761955,"version":"build-2736575974"},"reference-count":55,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:00:00Z","timestamp":1783555200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Genomics"],"published-print":{"date-parts":[[2026,8]]},"DOI":"10.1016\/j.xgen.2026.101323","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T15:13:35Z","timestamp":1786029215000},"page":"101323","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Automatic generation of model sequences for complex regions in assembly graphs with TTT"],"prefix":"10.1016","volume":"6","author":[{"given":"Dmitry","family":"Antipov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Sollitto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2983-8934","authenticated-orcid":false,"given":"Adam M.","family":"Phillippy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7554-5991","authenticated-orcid":false,"given":"Giulio","family":"Formenti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1472-8962","authenticated-orcid":false,"given":"Sergey","family":"Koren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xgen.2026.101323_bib1","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.xgen.2026.101323_bib2","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xgen.2026.101323_bib3","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/s41587-023-01662-6","article-title":"Telomere-to-telomere assembly of diploid chromosomes with Verkko","volume":"41","author":"Rautiainen","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2026.101323_bib4","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1038\/s41592-024-02269-8","article-title":"Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph","volume":"21","author":"Cheng","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xgen.2026.101323_bib5","first-page":"454","article-title":"Phased nanopore assembly with Shasta and modular graph phasing with GFAse","volume":"34","author":"Lorig-Roach","year":"2024","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2026.101323_bib6","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1101\/gr.280383.124","article-title":"Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding","volume":"35","author":"Antipov","year":"2025","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2026.101323_bib7","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/s41576-024-00718-w","article-title":"Genome assembly in the telomere-to-telomere era","volume":"25","author":"Li","year":"2024","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.xgen.2026.101323_bib8","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae124","article-title":"Ribotin: automated assembly and phasing of rDNA morphs","volume":"40","author":"Rautiainen","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2026.101323_bib9","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1038\/nbt.4277","article-title":"De novo assembly of haplotype-resolved genomes with trio binning","volume":"36","author":"Koren","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2026.101323_bib10","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s41587-020-0711-0","article-title":"Chromosome-scale, haplotype-resolved assembly of human genomes","volume":"39","author":"Garg","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2026.101323_bib11","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/s41586-025-08816-3","article-title":"Complete sequencing of ape genomes","volume":"641","author":"Yoo","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2026.101323_bib12","article-title":"Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens","author":"Olagunju","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.xgen.2026.101323_bib13","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1038\/s41588-024-01830-7","article-title":"Unlocking plant genetics with telomere-to-telomere genome assemblies","volume":"56","author":"Garg","year":"2024","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xgen.2026.101323_bib14","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1016\/j.ajhg.2023.09.011","article-title":"Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes","volume":"110","author":"Miga","year":"2023","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.xgen.2026.101323_bib15","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy157","article-title":"LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly","volume":"8","author":"Xu","year":"2019","journal-title":"GigaScience"},{"key":"10.1016\/j.xgen.2026.101323_bib16","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa094","article-title":"TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads","volume":"9","author":"Xu","year":"2020","journal-title":"GigaScience"},{"key":"10.1016\/j.xgen.2026.101323_bib17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009860","article-title":"The SAMBA tool uses long reads to improve the contiguity of genome assemblies","volume":"18","author":"Zimin","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.xgen.2026.101323_bib18","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbae194","article-title":"DEGAP: Dynamic elongation of a genome assembly path","volume":"25","author":"Huang","year":"2024","journal-title":"Brief. Bioinform."},{"key":"10.1016\/j.xgen.2026.101323_bib19","doi-asserted-by":"crossref","first-page":"127","DOI":"10.3390\/genes15010127","article-title":"Comprehensive evaluation of genome gap-filling tools utilizing long reads","volume":"15","author":"Zhao","year":"2024","journal-title":"Genes"},{"key":"10.1016\/j.xgen.2026.101323_bib20","article-title":"Approaching an Error-Free Diploid Human Genome Using a Support-Based Validation Framework","author":"Chu","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.xgen.2026.101323_bib21","doi-asserted-by":"crossref","first-page":"101279","DOI":"10.1016\/j.xgen.2026.101279","article-title":"Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet","volume":"6","author":"Kim","year":"2026","journal-title":"Cell Genomics"},{"key":"10.1016\/j.xgen.2026.101323_bib22","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/BF01585518","article-title":"On the existence of optimal solutions to integer and mixed-integer programming problems","volume":"7","author":"Meyer","year":"1974","journal-title":"Math. Program."},{"key":"10.1016\/j.xgen.2026.101323_bib23","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/BF01262932","article-title":"Integer and mixed-integer programming models: General properties","volume":"16","author":"Meyer","year":"1975","journal-title":"J. Optim. Theory Appl."},{"key":"10.1016\/j.xgen.2026.101323_bib24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cell.2026.06.016","article-title":"A complete diploid human genome benchmark for personalized genomics","volume":"189","author":"Hansen","year":"2026","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2026.101323_bib25","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":"10.1016\/j.xgen.2026.101323_bib26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cell.2026.07.018","article-title":"The complete genome of a songbird","volume":"189","author":"Formenti","year":"2026","journal-title":"Cell"},{"key":"10.1016\/j.xgen.2026.101323_bib35","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2026.101323_bib28","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1093\/molbev\/msq080","article-title":"Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata","volume":"27","author":"Kong","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.xgen.2026.101323_bib27","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/nature08819","article-title":"The genome of a songbird","volume":"464","author":"Warren","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.xgen.2026.101323_bib29","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1186\/1471-2164-15-1082","article-title":"Comparative genomics reveals molecular features unique to the songbird lineage","volume":"15","author":"Wirthlin","year":"2014","journal-title":"BMC Genom."},{"key":"10.1016\/j.xgen.2026.101323_bib30","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1007\/s00412-010-0308-3","article-title":"Karyotypic polymorphism of the zebra finch Z chromosome","volume":"120","author":"Itoh","year":"2011","journal-title":"Chromosoma"},{"key":"10.1016\/j.xgen.2026.101323_bib31","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-016-1056-3","article-title":"Fitness consequences of polymorphic inversions in the zebra finch genome","volume":"17","author":"Knief","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.xgen.2026.101323_bib32","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1038\/s41559-017-0235-2","article-title":"A sex-linked supergene controls sperm morphology and swimming speed in a songbird","volume":"1","author":"Kim","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.xgen.2026.101323_bib33","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/s41559-017-0236-1","article-title":"A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success","volume":"1","author":"Knief","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.xgen.2026.101323_bib34","doi-asserted-by":"crossref","DOI":"10.1111\/mec.17236","article-title":"Impact of Z chromosome inversions on gene expression in testis and liver tissues in the zebra finch","volume":"33","author":"Viitaniemi","year":"2024","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.xgen.2026.101323_bib36","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/bioinformatics\/btaa1016","article-title":"Liftoff: accurate mapping of gene annotations","volume":"37","author":"Shumate","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2026.101323_bib37","article-title":"A global view of human centromere variation and evolution","author":"Gao","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.xgen.2026.101323_bib38","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.xgen.2026.101323_bib39","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Kie\u0142basa","year":"2011","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2026.101323_bib40","article-title":"Protein-to-genome alignment with miniprot","volume":"39","author":"Li","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2026.101323_bib41","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae493","article-title":"ModDotPlot-rapid and interactive visualization of tandem repeats","volume":"40","author":"Sweeten","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2026.101323_bib42","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.xgen.2026.101323_bib43","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1089\/cmb.2014.0160","article-title":"On the representation of de Bruijn graphs","volume":"22","author":"Chikhi","year":"2015","journal-title":"J. Comput. Biol."},{"key":"10.1016\/j.xgen.2026.101323_bib44","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":"10.1016\/j.xgen.2026.101323_bib45","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/s41587-022-01220-6","article-title":"Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads","volume":"40","author":"Bankevich","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xgen.2026.101323_bib46","doi-asserted-by":"crossref","first-page":"i146","DOI":"10.1093\/bioinformatics\/btaa446","article-title":"Distance indexing and seed clustering in sequence graphs","volume":"36","author":"Chang","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xgen.2026.101323_bib47","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0066621","article-title":"Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies","volume":"8","author":"Rieber","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.xgen.2026.101323_bib48","article-title":"Highly accurate long-read HiFi sequencing data for five complex genomes","author":"Hon","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.xgen.2026.101323_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0257521","article-title":"Sequencing DNA with nanopores: Troubles and biases","volume":"16","author":"Delahaye","year":"2021","journal-title":"PLoS One"},{"key":"10.1016\/j.xgen.2026.101323_bib50","first-page":"71","article-title":"Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes","volume":"36","author":"Carvalho","year":"2026","journal-title":"Genome Res."},{"key":"10.1016\/j.xgen.2026.101323_bib51","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1145\/322276.322287","article-title":"On the complexity of integer programming","volume":"28","author":"Papadimitriou","year":"1981","journal-title":"J. ACM"},{"key":"10.1016\/j.xgen.2026.101323_bib52","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/BF01442866","article-title":"\u00dcber die M\u00f6glichkeit, einen Linienzug ohne Wiederholung und ohne Unterbrechung zu umfahren","volume":"6","author":"Hierholzer","year":"1873","journal-title":"Math. Ann."},{"key":"10.1016\/j.xgen.2026.101323_bib53","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/s13059-020-02157-2","article-title":"GraphAligner: rapid and versatile sequence-to-graph alignment","volume":"21","author":"Rautiainen","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.xgen.2026.101323_bib54","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching","volume":"18","author":"Aho","year":"1975","journal-title":"Commun. ACM"},{"key":"10.1016\/j.xgen.2026.101323_bib55","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/s41592-018-0236-3","article-title":"Long-read sequence and assembly of segmental duplications","volume":"16","author":"Vollger","year":"2019","journal-title":"Nat. Methods"}],"container-title":["Cell Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666979X26001850?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666979X26001850?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T19:37:58Z","timestamp":1786995478000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666979X26001850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8]]},"references-count":55,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8]]}},"alternative-id":["S2666979X26001850"],"URL":"https:\/\/doi.org\/10.1016\/j.xgen.2026.101323","relation":{},"ISSN":["2666-979X"],"issn-type":[{"value":"2666-979X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Automatic generation of model sequences for complex regions in assembly graphs with TTT","name":"articletitle","label":"Article Title"},{"value":"Cell Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xgen.2026.101323","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101323"}}