{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T22:06:42Z","timestamp":1774649202739,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,13]],"date-time":"2017-05-13T00:00:00Z","timestamp":1494633600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005847","name":"Health and Medical Research Fund","doi-asserted-by":"publisher","award":["12110542"],"award-info":[{"award-number":["12110542"]}],"id":[{"id":"10.13039\/501100005847","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Optical mapping is a molecular technique capturing specific patterns of fluorescent labels along DNA molecules. It has been widely applied in assisted-scaffolding in sequence assemblies, microbial strain typing and detection of structural variations. Various computational methods have been developed to analyze optical mapping data. However, existing tools for processing and visualizing optical map data still have many shortcomings. Here, we present OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>OMTools is implemented in Java 1.8 and released under a GPL license. OMTools can be downloaded from https:\/\/github.com\/aldenleung\/OMTools and run on any standard desktop computer equipped with a Java virtual machine.<\/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\/btx317","type":"journal-article","created":{"date-parts":[[2017,5,12]],"date-time":"2017-05-12T03:10:51Z","timestamp":1494558651000},"page":"2933-2935","source":"Crossref","is-referenced-by-count":32,"title":["OMTools: a software package for visualizing and processing optical mapping data"],"prefix":"10.1093","volume":"33","author":[{"given":"Alden King-Yung","family":"Leung","sequence":"first","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China"},{"name":"Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Nana","family":"Jin","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China"},{"name":"Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Kevin Y","family":"Yip","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China"},{"name":"Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China"}]}],"member":"286","published-online":{"date-parts":[[2017,5,12]]},"reference":[{"key":"2023020206412840700_btx317-B1","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/2047-217X-3-34","article-title":"Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology","volume":"3","author":"Cao","year":"2014","journal-title":"Gigascience"},{"key":"2023020206412840700_btx317-B2","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/nbt.2478","article-title":"Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)","volume":"31","author":"Dong","year":"2013","journal-title":"Nat. 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Biotechnol"},{"key":"2023020206412840700_btx317-B4","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btw620","article-title":"OMBlast: alignment tool for optical mapping using a seed-and-extend approach","volume":"33","author":"Leung","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020206412840700_btx317-B5","doi-asserted-by":"crossref","first-page":"351\u2013362","DOI":"10.1534\/genetics.115.183483","article-title":"Genome-wide structural variation detection by genome mapping on nanochannel arrays","volume":"202","author":"Mak","year":"2016","journal-title":"Genetics"},{"key":"2023020206412840700_btx317-B6","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1099\/mic.0.033977-0","article-title":"Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups","volume":"156","author":"Schwan","year":"2010","journal-title":"Microbiology"},{"key":"2023020206412840700_btx317-B7","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1186\/s12864-015-1911-8","article-title":"Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool","volume":"16","author":"Shelton","year":"2015","journal-title":"BMC Genomics"},{"key":"2023020206412840700_btx317-B8","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"Skinner","year":"2009","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2933\/49041057\/bioinformatics_33_18_2933.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2933\/49041057\/bioinformatics_33_18_2933.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:41:40Z","timestamp":1675320100000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/18\/2933\/3823311"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,12]]},"references-count":8,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2017,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx317","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,15]]},"published":{"date-parts":[[2017,5,12]]}}}