{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T16:39:44Z","timestamp":1772642384405,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,13]],"date-time":"2019-12-13T00:00:00Z","timestamp":1576195200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020","award":["ERC-2016-724173"],"award-info":[{"award-number":["ERC-2016-724173"]}]},{"name":"Spanish Ministry of Economy, Industry, and Competitiveness"},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Catalan Research Agency","award":["SGR857"],"award-info":[{"award-number":["SGR857"]}]},{"name":"Catalan Research Agency","award":["PT17\/0009\/0023\u2014ISCIII-SGEFI\/ERDF"],"award-info":[{"award-number":["PT17\/0009\/0023\u2014ISCIII-SGEFI\/ERDF"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https:\/\/github.com\/gabaldonlab\/haplotypo, and as a Docker image.<\/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\/btz933","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T20:12:14Z","timestamp":1576008734000},"page":"2569-2571","source":"Crossref","is-referenced-by-count":16,"title":["HaploTypo: a variant-calling pipeline for phased genomes"],"prefix":"10.1093","volume":"36","author":[{"given":"Cinta","family":"Pegueroles","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ver\u00f3nica","family":"Mix\u00e3o","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laia","family":"Carret\u00e9","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manu","family":"Molina","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0019-1735","authenticated-orcid":false,"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona, Spain"},{"name":"ICREA , Barcelona 08010, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,13]]},"reference":[{"key":"2023013110261076300_btz933-B1","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1534\/genetics.118.301482","article-title":"Diverse lineages of live on old oaks","volume":"211","author":"Bensasson","year":"2019","journal-title":"Genetics"},{"key":"2023013110261076300_btz933-B2","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nmeth.4035","article-title":"Phased diploid genome assembly with single-molecule real-time sequencing","volume":"13","author":"Chin","year":"2016","journal-title":"Nat. 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