{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T04:31:08Z","timestamp":1786681868854,"version":"3.56.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T00:00:00Z","timestamp":1671148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome","doi-asserted-by":"publisher","award":["207492"],"award-info":[{"award-number":["207492"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome","doi-asserted-by":"publisher","award":["218328"],"award-info":[{"award-number":["218328"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome","doi-asserted-by":"publisher","award":["220540"],"award-info":[{"award-number":["220540"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>YaHS is implemented in C and licensed under the MIT License. The source code, documentation and tutorial are available at https:\/\/github.com\/sanger-tol\/yahs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac808","type":"journal-article","created":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T13:11:08Z","timestamp":1671196268000},"source":"Crossref","is-referenced-by-count":2414,"title":["YaHS: yet another Hi-C scaffolding tool"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1735-2630","authenticated-orcid":false,"given":"Chenxi","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK"},{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2715-4187","authenticated-orcid":false,"given":"Shane A","family":"McCarthy","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK"},{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9130-1006","authenticated-orcid":false,"given":"Richard","family":"Durbin","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of Cambridge , Cambridge CB2 3EH, UK"},{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,16]]},"reference":[{"key":"2023011906410758300_btac808-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2023011906410758300_btac808-B2","article-title":"Sequence locally, think globally: the Darwin Tree of Life Project","volume":"119","author":"Blaxter","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023011906410758300_btac808-B3","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/nbt.2727","article-title":"Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions","volume":"31","author":"Burton","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023011906410758300_btac808-B4","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"2023011906410758300_btac808-B5","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2023011906410758300_btac808-B6","doi-asserted-by":"crossref","first-page":"e1007273","DOI":"10.1371\/journal.pcbi.1007273","article-title":"Integrating Hi-C links with assembly graphs for chromosome-scale assembly","volume":"15","author":"Ghurye","year":"2019","journal-title":"PLoS Comput. Biol"},{"key":"2023011906410758300_btac808-B7","first-page":"1","article-title":"Efficient iterative Hi-C scaffolder based on N-best neighbors","volume":"22","author":"Guan","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2023011906410758300_btac808-B8","article-title":"Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?","volume":"9, giz158","author":"Kadota","year":"2020","journal-title":"Gigascience"},{"key":"2023011906410758300_btac808-B9","doi-asserted-by":"crossref","first-page":"4325","DOI":"10.1073\/pnas.1720115115","article-title":"Earth Biogenome Project: sequencing life for the future of life","volume":"115","author":"Lewin","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023011906410758300_btac808-B10","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2023011906410758300_btac808-B11","doi-asserted-by":"crossref","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","article-title":"Versatile genome assembly evaluation with QUAST-LG","volume":"34","author":"Mikheenko","year":"2018","journal-title":"Bioinformatics"},{"key":"2023011906410758300_btac808-B12","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":"2023011906410758300_btac808-B13","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1101\/gr.193474.115","article-title":"Chromosome-scale shotgun assembly using an in vitro method for long-range linkage","volume":"26","author":"Putnam","year":"2016","journal-title":"Genome Res"},{"key":"2023011906410758300_btac808-B14","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"key":"2023011906410758300_btac808-B15","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/s41477-019-0487-8","article-title":"Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data","volume":"5","author":"Zhang","year":"2019","journal-title":"Nat. Plants"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/39\/1\/btac808\/48759250\/btac808.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac808\/48763581\/btac808.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac808\/48763581\/btac808.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T01:43:24Z","timestamp":1674092604000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac808\/6917071"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,12,16]]},"references-count":15,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac808","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.09.495093","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,12,16]]},"article-number":"btac808"}}