{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T07:46:10Z","timestamp":1770277570358,"version":"3.49.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T00:00:00Z","timestamp":1612396800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Qingdao Applied Basic Research Projects","award":["19-6-2-33-cg"],"award-info":[{"award-number":["19-6-2-33-cg"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFD0900301-05"],"award-info":[{"award-number":["2018YFD0900301-05"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Achieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assemble the parent-specific haplotypes. We applied HAST to cobarcoded second-generation sequencing data from an Asian individual, resulting in a haplotype assembly covering 94.7% of the reference genome with a scaffold N50 longer than 11\u2009Mb. The high haplotyping precision (\u223c99.7%) and recall (\u223c95.9%) represents a substantial improvement over the commonly used tool for assembling cobarcoded reads (Supernova), and is comparable to a trio-binning-based third generation long-read-based assembly method (TrioCanu) but with a significantly higher single-base accuracy [up to 99.99997% (Q65)]. This makes HAST a superior tool for accurate haplotyping and future haplotype-based studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code of the analysis is available at https:\/\/github.com\/BGI-Qingdao\/HAST<\/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\/btab068","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T18:40:40Z","timestamp":1611859240000},"page":"2095-2102","source":"Crossref","is-referenced-by-count":8,"title":["Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4487-7088","authenticated-orcid":false,"given":"Mengyang","family":"Xu","sequence":"first","affiliation":[{"name":"BGI-QingDao , Qingdao 266555, China"},{"name":"BGI-Shenzhen , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lidong","family":"Guo","sequence":"additional","affiliation":[{"name":"BGI-QingDao , Qingdao 266555, China"},{"name":"BGI Education Center, University of Chinese Academy of Sciences , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Du","sequence":"additional","affiliation":[{"name":"BGI-QingDao , Qingdao 266555, China"},{"name":"BGI-Shenzhen , Shenzhen 518083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Li","sequence":"additional","affiliation":[{"name":"BGI-QingDao , Qingdao 266555, China"},{"name":"School of Future Technology, University 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