{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T05:54:40Z","timestamp":1722750880278},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,6,3]],"date-time":"2016-06-03T00:00:00Z","timestamp":1464912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"National Agency for the Advancement of Science and Technology of Argentina","award":["PICT 2012-2513"],"award-info":[{"award-number":["PICT 2012-2513"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10\u22127 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar\/ezpeleta\/NS-watermark.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw322","type":"journal-article","created":{"date-parts":[[2016,6,4]],"date-time":"2016-06-04T00:43:35Z","timestamp":1465001015000},"page":"807-813","source":"Crossref","is-referenced-by-count":3,"title":["Designing robust watermark barcodes for multiplex long-read sequencing"],"prefix":"10.1093","volume":"33","author":[{"given":"Joaqu\u00edn","family":"Ezpeleta","sequence":"first","affiliation":[{"name":"Centro Internacional Franco Argentino de Ciencias de la Informaci\u00f3n y de Sistemas, Rosario, Argentina"},{"name":"Facultad de Ciencias Exactas, Ingenier\u00eda y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina"}]},{"given":"Flavia J","family":"Krsticevic","sequence":"additional","affiliation":[{"name":"Centro Internacional Franco Argentino de Ciencias de la Informaci\u00f3n y de Sistemas, Rosario, Argentina"}]},{"given":"Pilar","family":"Bulacio","sequence":"additional","affiliation":[{"name":"Centro Internacional Franco Argentino de Ciencias de la Informaci\u00f3n y de Sistemas, Rosario, Argentina"},{"name":"Facultad de Ciencias Exactas, Ingenier\u00eda y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina"}]},{"given":"Elizabeth","family":"Tapia","sequence":"additional","affiliation":[{"name":"Centro Internacional Franco Argentino de Ciencias de la Informaci\u00f3n y de Sistemas, Rosario, Argentina"},{"name":"Facultad de Ciencias Exactas, Ingenier\u00eda y Agrimensura, Universidad Nacional de Rosario, Rosario, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2016,6,3]]},"reference":[{"key":"2023020204511550100_btw322-B1","doi-asserted-by":"crossref","first-page":"3227","DOI":"10.1016\/S0006-3495(99)77153-5","article-title":"Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules","volume":"77","author":"Akeson","year":"1999","journal-title":"Biophys. 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