{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T20:03:39Z","timestamp":1775505819168,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,5,4]],"date-time":"2020-05-04T00:00:00Z","timestamp":1588550400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"University of Minnesota Masonic Cancer Center"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI121383"],"award-info":[{"award-number":["R01AI121383"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01DK078669"],"award-info":[{"award-number":["P01DK078669"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1565057"],"award-info":[{"award-number":["1565057"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Masonic Cancer Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/knights-lab\/SHOGUN.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa277","type":"journal-article","created":{"date-parts":[[2020,4,24]],"date-time":"2020-04-24T19:10:16Z","timestamp":1587755416000},"page":"4088-4090","source":"Crossref","is-referenced-by-count":64,"title":["SHOGUN: a modular, accurate and scalable framework for microbiome quantification"],"prefix":"10.1093","volume":"36","author":[{"given":"Benjamin","family":"Hillmann","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA"}]},{"given":"Gabriel A","family":"Al-Ghalith","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA"}]},{"given":"Robin R","family":"Shields-Cutler","sequence":"additional","affiliation":[{"name":"Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA"}]},{"given":"Qiyun","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0975-9019","authenticated-orcid":false,"given":"Rob","family":"Knight","sequence":"additional","affiliation":[{"name":"Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA"},{"name":"Department of Computer of Science and Engineering , University of California San Diego, San Diego, 92093 California, USA"},{"name":"Center for Microbiome Innovation , University of California San Diego, San Diego, 92093 California, USA"}]},{"given":"Dan","family":"Knights","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA"},{"name":"Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA"},{"name":"Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,5,4]]},"reference":[{"key":"2023062312040411900_btaa277-B1"},{"key":"2023062312040411900_btaa277-B2","author":"Al-Ghalith","year":"2017"},{"key":"2023062312040411900_btaa277-B3","author":"Al-Ghalith","year":"2017"},{"key":"2023062312040411900_btaa277-B4","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"Bateman","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023062312040411900_btaa277-B5","author":"Bolyen","year":"2018"},{"key":"2023062312040411900_btaa277-B6","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1016\/j.bbadis.2014.06.015","article-title":"Next generation sequencing technology: advances and applications","volume":"1842","author":"Buermans","year":"2014","journal-title":"Biochim. 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