{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:49Z","timestamp":1772138089653,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T00:00:00Z","timestamp":1527811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006067","name":"Australian Research Council Centre of Excellence in Plant Energy Biology","doi-asserted-by":"publisher","award":["CE140100008"],"award-info":[{"award-number":["CE140100008"]}],"id":[{"id":"10.13039\/501100006067","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010582","name":"National Computational Infrastructure","doi-asserted-by":"publisher","award":["NCI"],"award-info":[{"award-number":["NCI"]}],"id":[{"id":"10.13039\/100010582","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015539","name":"Australian Government","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100015539","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Australian Government Research Training Program"},{"name":"RTP"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length and several mismatches per index sequence.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Axe is implemented in C, and is used as a command-line program on Unix-like systems. Axe is available online at https:\/\/github.com\/kdmurray91\/axe, and is available in Debian\/Ubuntu distributions of GNU\/Linux as the package axe-demultiplexer.<\/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\/bty432","type":"journal-article","created":{"date-parts":[[2018,5,30]],"date-time":"2018-05-30T07:20:10Z","timestamp":1527664810000},"page":"3924-3925","source":"Crossref","is-referenced-by-count":70,"title":["Axe: rapid, competitive sequence read demultiplexing using a trie"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2466-1917","authenticated-orcid":false,"given":"Kevin D","family":"Murray","sequence":"first","affiliation":[{"name":"ARC Centre of Excellence in Plant Energy Biology, Department of Plant Science, Research School of Biology, ANU, Canberra, Australia"}]},{"given":"Justin O","family":"Borevitz","sequence":"additional","affiliation":[{"name":"ARC Centre of Excellence in Plant Energy Biology, Department of Plant Science, Research School of Biology, ANU, Canberra, Australia"}]}],"member":"286","published-online":{"date-parts":[[2018,6,1]]},"reference":[{"key":"2023012712341014400_bty432-B1","doi-asserted-by":"crossref","first-page":"895","DOI":"10.3390\/biology1030895","article-title":"FLEXBAR: flexible barcode and adapter processing for next-generation sequencing platforms","volume":"1","author":"Dodt","year":"2012","journal-title":"Biology"},{"key":"2023012712341014400_bty432-B2","doi-asserted-by":"crossref","first-page":"e19379.","DOI":"10.1371\/journal.pone.0019379","article-title":"A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species","volume":"6","author":"Elshire","year":"2011","journal-title":"PLoS One"},{"key":"2023012712341014400_bty432-B3","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1002\/j.1538-7305.1950.tb00463.x","article-title":"Error detecting and error correcting codes","volume":"29","author":"Hamming","year":"1950","journal-title":"Bell Syst. 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Notes"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3924\/48920085\/bioinformatics_34_22_3924.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3924\/48920085\/bioinformatics_34_22_3924.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:23:40Z","timestamp":1674807820000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/22\/3924\/5026649"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,1]]},"references-count":7,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2018,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty432","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/160606","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,11,15]]},"published":{"date-parts":[[2018,6,1]]}}}