{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T11:17:50Z","timestamp":1758280670202,"version":"3.41.2"},"reference-count":106,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T00:00:00Z","timestamp":1718928000000},"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":[[2024,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Long-range sequencing grants insight into additional genetic information beyond what can be accessed by both short reads and modern long-read technology. Several new sequencing technologies, such as \u201cHi-C\u201d and \u201cLinked Reads\u201d, produce long-range datasets for high-throughput and high-resolution genome analyses, which are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this review, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-C), 10X Genomics Linked Reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single- tube long fragment read (stLFR). We detailed the mechanisms and data products of the five platforms and their important applications, evaluated the quality of sequencing data from different platforms, and discussed the currently available bioinformatics tools. This work will benefit the selection of appropriate long-range technology for specific biological studies.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae048","type":"journal-article","created":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T19:19:01Z","timestamp":1718997541000},"source":"Crossref","is-referenced-by-count":3,"title":["The Bioinformatic Applications of Hi-C and Linked Reads"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4703-9220","authenticated-orcid":false,"given":"Libo","family":"Jiang","sequence":"first","affiliation":[{"name":"School of Life Sciences and Medicine, Shandong University of Technology , Zibo 255049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3861-0483","authenticated-orcid":false,"given":"Michael A","family":"Quail","sequence":"additional","affiliation":[{"name":"The Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SA,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6980-8484","authenticated-orcid":false,"given":"Jack","family":"Fraser-Govil","sequence":"additional","affiliation":[{"name":"The Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SA,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2366-7946","authenticated-orcid":false,"given":"Haipeng","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Medicine, Shandong University of Technology , Zibo 255049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6495-241X","authenticated-orcid":false,"given":"Xuequn","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Food Science and Technology, Hainan University , Haikou 570228,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8329-2284","authenticated-orcid":false,"given":"Karen","family":"Oliver","sequence":"additional","affiliation":[{"name":"The Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SA,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7168-1734","authenticated-orcid":false,"given":"Esther","family":"Mellado Gomez","sequence":"additional","affiliation":[{"name":"The Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton, Cambridge CB10 1SA,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3573-2354","authenticated-orcid":false,"given":"Fengtang","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Medicine, Shandong University of Technology , Zibo 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carcinomas","volume":"13","author":"Tan","year":"2021","journal-title":"Genome Med"},{"key":"2024112116012981700_qzae048-B60","doi-asserted-by":"crossref","first-page":"332","DOI":"10.3390\/genes11030332","article-title":"A comparison between Hi-C and 10X Genomics Linked Read sequencing for whole genome phasing in Hanwoo cattle","volume":"11","author":"Srikanth","year":"2020","journal-title":"Genes"},{"key":"2024112116012981700_qzae048-B61","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/s40168-020-00929-3","article-title":"A comprehensive investigation of metagenome assembly by linked-read sequencing","volume":"8","author":"Zhang","year":"2020","journal-title":"Microbiome"},{"key":"2024112116012981700_qzae048-B62","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1101\/gr.265058.120","article-title":"Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic 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