{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T13:53:48Z","timestamp":1770299628513,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T00:00:00Z","timestamp":1732665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62350004"],"award-info":[{"award-number":["62350004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62332020"],"award-info":[{"award-number":["62332020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Project of Xiangjiang Laboratory","award":["23XJ01011"],"award-info":[{"award-number":["23XJ01011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Haplotype-resolved genome assemblies serve as vital resources in various research domains, including genomics, medicine, and pangenomics. Algorithms employing Hi-C data to generate haplotype-resolved assemblies are particularly advantageous due to its ready availability. Existing methods primarily depend on mapping quality to filter out uninformative Hi-C alignments which may be susceptible to sequencing errors. Setting a high mapping quality threshold filters out numerous informative Hi-C alignments, whereas a low mapping quality threshold compromises the accuracy of Hi-C alignments. Maintaining high accuracy while retaining a maximum number of Hi-C alignments can be challenging.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In our experiments, heterozygous variations play an important role in filtering uninformative Hi-C alignments. Here, we introduce Diphase, a novel phasing tool that harnesses heterozygous variations to accurately identify the informative Hi-C alignments for phasing and to extend primary\/alternate assemblies. Diphase leverages mapping quality and heterozygous variations to filter uninformative Hi-C alignments, thereby enhancing the accuracy of phasing and the detection of switches. To validate its performance, we conducted a comparative analysis of Diphase, FALCON-Phase, and GFAse on various human datasets. The results demonstrate that Diphase achieves a longer phased block N50 and exhibits higher phasing accuracy while maintaining a lower hamming error rate.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of Diphase is available at https:\/\/github.com\/zhangjuncsu\/Diphase<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae712","type":"journal-article","created":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T21:49:35Z","timestamp":1732744175000},"source":"Crossref","is-referenced-by-count":1,"title":["Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data"],"prefix":"10.1093","volume":"40","author":[{"given":"Jun","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083,","place":["China"]},{"name":"Xiangjiang Laboratory , Changsha, Hunan 410205,","place":["China"]},{"name":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha, Hunan 410083,","place":["China"]}]},{"given":"Fan","family":"Nie","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083,","place":["China"]},{"name":"Xiangjiang Laboratory , Changsha, Hunan 410205,","place":["China"]},{"name":"Hunan Provincial Key Lab on Bioinformatics, Central South University , Changsha, Hunan 410083,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4813-2403","authenticated-orcid":false,"given":"Feng","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Computing, Clemson University , Clemson, SC 29634-0974,","place":["United 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