{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T07:55:16Z","timestamp":1778658916188,"version":"3.51.4"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,25]],"date-time":"2018-08-25T00:00:00Z","timestamp":1535155200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"France G\u00e9nomique consortium","award":["ANR10-INBS-09-08"],"award-info":[{"award-number":["ANR10-INBS-09-08"]}]},{"name":"France G\u00e9nomique consortium","award":["ANR-10-INBS-09-10"],"award-info":[{"award-number":["ANR-10-INBS-09-10"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>When sequencing several libraries simultaneously, the selection of compatible combinations of indexes is critical for ensuring that the sequencer will be able to decipher the short, sample-specific barcodes added to each fragment. However, researchers have few tools to help them choose optimal indexes. Here, we present checkMyIndex, an online R\/Shiny application that facilitates the selection of the right indexes as a function of the experimental constraints.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>checkMyIndex is available free of charge at https:\/\/checkmyindex.pasteur.fr as an online, web-based R\/Shiny application. The source code is available on GitHub at https:\/\/github.com\/PF2-pasteur-fr\/checkMyIndex.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty706","type":"journal-article","created":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T19:31:23Z","timestamp":1535052683000},"page":"901-902","source":"Crossref","is-referenced-by-count":5,"title":["checkMyIndex: a web-based R\/Shiny interface for choosing compatible sequencing indexes"],"prefix":"10.1093","volume":"35","author":[{"given":"Hugo","family":"Varet","sequence":"first","affiliation":[{"name":"Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur \u2013 Bioinformatics and Biostatistics Hub \u2013 C3BI, USR 3756 IP CNRS, Paris, France"},{"name":"Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Yves","family":"Copp\u00e9e","sequence":"additional","affiliation":[{"name":"Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,25]]},"reference":[{"key":"2023013107250253200_bty706-B1","volume-title":"Shiny: Web Application Framework for R. R Package Version 1.0.5","author":"Chang","year":"2017"},{"key":"2023013107250253200_bty706-B2","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023013107250253200_bty706-B3","doi-asserted-by":"crossref","first-page":"e3.","DOI":"10.1093\/nar\/gkr771","article-title":"Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform","volume":"40","author":"Kircher","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/901\/48965813\/bioinformatics_35_5_901.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/901\/48965813\/bioinformatics_35_5_901.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T09:58:05Z","timestamp":1675159085000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/5\/901\/5079327"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,25]]},"references-count":3,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty706","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3,1]]},"published":{"date-parts":[[2018,8,25]]}}}