{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:18Z","timestamp":1772138058881,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,10,29]],"date-time":"2022-10-29T00:00:00Z","timestamp":1667001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Haplotypes are the set of alleles co-occurring on a single chromosome and inherited together to the next generation. Because a monoploid reference genome loses this co-occurrence information, it has limited use in associating phenotypes with allelic combinations of genotypes. Therefore, methods to reconstruct the complete haplotypes from DNA sequencing data are crucial. Recently, several attempts have been made at haplotype reconstructions, but significant limitations remain. High-quality continuous haplotypes cannot be created reliably, particularly when there are few differences between the homologous chromosomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduce HAT, a haplotype assembly tool that exploits short and long reads along with a reference genome to reconstruct haplotypes. HAT tries to take advantage of the accuracy of short reads and the length of the long reads to reconstruct haplotypes. We tested HAT on the aneuploid yeast strain Saccharomyces pastorianus CBS1483 and multiple simulated polyploid datasets of the same strain, showing that it outperforms existing tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/AbeelLab\/hat\/.<\/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\/btac702","type":"journal-article","created":{"date-parts":[[2022,10,29]],"date-time":"2022-10-29T09:47:44Z","timestamp":1667036864000},"page":"5352-5359","source":"Crossref","is-referenced-by-count":0,"title":["HAT: haplotype assembly tool using short and error-prone long reads"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2624-0718","authenticated-orcid":false,"given":"Ramin","family":"Shirali Hossein Zade","sequence":"first","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology Van Mourik , 2628 XE Delft, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aysun","family":"Urhan","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology Van Mourik , 2628 XE Delft, The Netherlands"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alvaro","family":"Assis de Souza","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology Van Mourik , 2628 XE Delft, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akash","family":"Singh","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology Van Mourik , 2628 XE Delft, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-7431","authenticated-orcid":false,"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology Van Mourik , 2628 XE Delft, The Netherlands"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,29]]},"reference":[{"key":"2022121418364937600_btac702-B1","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/s13059-021-02342-x","article-title":"nPhase: an accurate and contiguous phasing method for polyploids","volume":"22","author":"Abou Saada","year":"2021","journal-title":"Genome Biol"},{"key":"2022121418364937600_btac702-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-021-02782-y","article-title":"Features and applications of haplotypes in crop breeding","volume":"4","author":"Bhat","year":"2021","journal-title":"Commun. Biol"},{"key":"2022121418364937600_btac702-B3","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1146\/annurev.med.56.082103.104540","article-title":"Definition and clinical importance of haplotypes","volume":"56","author":"Crawford","year":"2005","journal-title":"Annu. Rev. Med"},{"key":"2022121418364937600_btac702-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-021-02328-9","article-title":"Computational methods for chromosome-scale haplotype reconstruction","volume":"22","author":"Garg","year":"2021","journal-title":"Genome Biol"},{"key":"2022121418364937600_btac702-B7","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2022121418364937600_btac702-B8","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":"2022121418364937600_btac702-B9","doi-asserted-by":"crossref","first-page":"e1007843","DOI":"10.1371\/journal.pcbi.1007843","article-title":"Ranbow: a fast and accurate method for polyploid haplotype reconstruction","volume":"16","author":"Moeinzadeh","year":"2020","journal-title":"PLoS Comput. Biol"},{"key":"2022121418364937600_btac702-B10","first-page":"387","article-title":"Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study","volume":"19","author":"Motazedi","year":"2018","journal-title":"Brief. Bioinform"},{"key":"2022121418364937600_btac702-B11","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nature08250","article-title":"Targeted capture and massively parallel sequencing of 12 human exomes","volume":"461","author":"Ng","year":"2009","journal-title":"Nature"},{"key":"2022121418364937600_btac702-B12","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1146\/annurev.ecolsys.29.1.467","article-title":"Pathways, mechanisms, and rates of polyploid formation in flowering plants","volume":"29","author":"Ramsey","year":"1998","journal-title":"Annu. Rev. Ecol. Syst"},{"key":"2022121418364937600_btac702-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-019-6263-3","article-title":"Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization","volume":"20","author":"Salazar","year":"2019","journal-title":"BMC Genomics"},{"key":"2022121418364937600_btac702-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-02158-1","article-title":"Haplotype threading: accurate polyploid phasing from long reads","volume":"21","author":"Schrinner","year":"2020","journal-title":"Genome Biol"},{"key":"2022121418364937600_btac702-B15","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res"},{"key":"2022121418364937600_btac702-B16","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"2022121418364937600_btac702-B17","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.21105\/joss.01316","article-title":"Badread: simulation of error-prone long reads","volume":"4","author":"Wick","year":"2019","journal-title":"J. Open Source Softw"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac702\/46874689\/btac702.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/24\/5352\/47886904\/btac702.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/24\/5352\/47886904\/btac702.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,14]],"date-time":"2022-12-14T13:37:22Z","timestamp":1671025042000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/24\/5352\/6779972"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,10,29]]},"references-count":15,"journal-issue":{"issue":"24","published-online":{"date-parts":[[2022,10,29]]},"published-print":{"date-parts":[[2022,12,13]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac702","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.07.20.500775","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":[[2022,12,15]]},"published":{"date-parts":[[2022,10,29]]}}}