{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T15:38:10Z","timestamp":1775662690257,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T00:00:00Z","timestamp":1540425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Union\u2019s Horizon 2020","award":["634650"],"award-info":[{"award-number":["634650"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>UGENE is a free, open-source, cross-platform bioinformatics software. UGENE deploys pre-defined pipelines and a flexible instrument to design new workflows and visually build multi-step analytics pipelines. The new UGENE v.1.31 release offers graphical, user-friendly wrapping of a number of popular command-line metagenomics classification programs (Kraken, CLARK, DIAMOND), combinable serially and in parallel through the workflow designer, with multiple, customizable reference databases. Ensemble classification voting is available through the WEVOTE algorithm, with augmented output in the form of detailed table reports. Pre-built workflows (which include all steps from data cleaning to summaries) are included with the installation and a tutorial is available on the UGENE website. Further expansion with multiple visualization tools for reports is planned.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>UGENE is available at http:\/\/ugene.net\/, implemented in C++ and Qt, and released under GNU General Public License (GPL) version 2.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty901","type":"journal-article","created":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T02:13:12Z","timestamp":1540433592000},"page":"1963-1965","source":"Crossref","is-referenced-by-count":82,"title":["Flexible design of multiple metagenomics classification pipelines with UGENE"],"prefix":"10.1093","volume":"35","author":[{"given":"Rebecca","family":"Rose","sequence":"first","affiliation":[{"name":"BioInfoExperts, LLC, Thibodaux, LA, USA"}]},{"given":"Olga","family":"Golosova","sequence":"additional","affiliation":[{"name":"UNIPRO, LLC, Novosibirsk, Russia"}]},{"given":"Dmitrii","family":"Sukhomlinov","sequence":"additional","affiliation":[{"name":"UNIPRO, LLC, Novosibirsk, Russia"}]},{"given":"Aleksey","family":"Tiunov","sequence":"additional","affiliation":[{"name":"UNIPRO, LLC, Novosibirsk, Russia"}]},{"given":"Mattia","family":"Prosperi","sequence":"additional","affiliation":[{"name":"University of Florida, Gainesville, FL, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,10,25]]},"reference":[{"key":"2023012713232228600_bty901-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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