{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T19:46:07Z","timestamp":1781725567210,"version":"3.54.5"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2017,4,12]],"date-time":"2017-04-12T00:00:00Z","timestamp":1491955200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (\u22653%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Source code, executables and the testing dataset are freely available at https:\/\/github.com\/mapleforest\/HaploMerger2\/releases\/.<\/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\/btx220","type":"journal-article","created":{"date-parts":[[2017,4,11]],"date-time":"2017-04-11T12:06:01Z","timestamp":1491912361000},"page":"2577-2579","source":"Crossref","is-referenced-by-count":196,"title":["HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly"],"prefix":"10.1093","volume":"33","author":[{"given":"Shengfeng","family":"Huang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People\u2019s Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingjing","family":"Kang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People\u2019s Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anlong","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People\u2019s Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,4,12]]},"reference":[{"key":"2023020206245224000_btx220-B1","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nbt.3238","article-title":"Assembling large genomes with single-molecule sequencing and locality-sensitive hashing","volume":"33","author":"Berlin","year":"2015","journal-title":"Nat. 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