{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:12:41Z","timestamp":1675321961950},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,8]],"date-time":"2017-05-08T00:00:00Z","timestamp":1494201600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The C\u2009++\u2009source code of rMFilter is available at https:\/\/github.com\/hitbc\/rMFilter.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx279","type":"journal-article","created":{"date-parts":[[2017,5,5]],"date-time":"2017-05-05T11:08:58Z","timestamp":1493982538000},"page":"2750-2752","source":"Crossref","is-referenced-by-count":0,"title":["rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering"],"prefix":"10.1093","volume":"33","author":[{"given":"Bo","family":"Liu","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China"}]},{"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China"}]},{"given":"S M","family":"Yiu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, The University of Hong Kong, Hong Kong, China"}]},{"given":"Junyi","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China"}]},{"given":"Yadong","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China"}]}],"member":"286","published-online":{"date-parts":[[2017,5,8]]},"reference":[{"key":"2023020206270738700_btx279-B1","doi-asserted-by":"crossref","first-page":"238.","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"Chaisson","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020206270738700_btx279-B2","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/nature13907","article-title":"Resolving the complexity of the human genome using single-molecule sequencing","volume":"517","author":"Chaisson","year":"2015","journal-title":"Nature"},{"key":"2023020206270738700_btx279-B3","doi-asserted-by":"crossref","first-page":"180.","DOI":"10.1186\/1471-2105-15-180","article-title":"PBHoney: identifying genomic variants via long-read discordance and interrupted mapping","volume":"15","author":"English","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020206270738700_btx279-B4","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1093\/bioinformatics\/btv662","article-title":"rHAT: fast alignment of noisy long reads with regional hashing","volume":"32","author":"Liu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020206270738700_btx279-B5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2750\/49040837\/bioinformatics_33_17_2750.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/17\/2750\/49040837\/bioinformatics_33_17_2750.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:29:11Z","timestamp":1675319351000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/17\/2750\/3803438"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,5,8]]},"references-count":5,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2017,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx279","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,1]]},"published":{"date-parts":[[2017,5,8]]}}}