{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T04:24:10Z","timestamp":1780979050201,"version":"3.54.1"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T00:00:00Z","timestamp":1570060800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T00:00:00Z","timestamp":1570060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n              <jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and current metagenomic technology supports assemblies of many draft-quality genomes from a single sample, most of which will be novel.<\/jats:p>\n              <\/jats:sec>\n              <jats:sec>\n                <jats:title>Description<\/jats:title>\n                <jats:p>We have added two quality assessment tools to the PATRIC annotation pipeline. EvalCon uses supervised machine learning to calculate an annotation consistency score. EvalG implements a variant of the CheckM algorithm to estimate contamination and completeness of an annotated genome.We report on the performance of these tools and the potential utility of the consistency score. Additionally, we provide contamination, completeness, and consistency measures for all genomes in PATRIC and in a recent set of metagenomic assemblies.<\/jats:p>\n              <\/jats:sec>\n              <jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>EvalG and EvalCon facilitate the rapid quality control and exploration of PATRIC-annotated draft genomes.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-019-3068-y","type":"journal-article","created":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T10:11:00Z","timestamp":1570097460000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["A machine learning-based service for estimating quality of genomes using PATRIC"],"prefix":"10.1186","volume":"20","author":[{"given":"Bruce","family":"Parrello","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rory","family":"Butler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2951-4385","authenticated-orcid":false,"given":"Philippe","family":"Chlenski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Olson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jamie","family":"Overbeek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon D.","family":"Pusch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Vonstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross","family":"Overbeek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,10,3]]},"reference":[{"issue":"D1","key":"3068_CR1","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1093\/nar\/gkw1017","volume":"45","author":"AR Wattam","year":"2017","unstructured":"Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard J, Gerdes S, Henry CS, Kenyon R, Machi D, Mao C, Nordberg EK, Olsen G, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens R. Improvements to patric, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res. 2017; 45(D1):535\u201342. \n                    https:\/\/doi.org\/10.1093\/nar\/gkw1017\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"3068_CR2","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1093\/nar\/gkl858","volume":"35","author":"EE Snyder","year":"2007","unstructured":"Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BWS. Patric: the vbi pathosystems resource integration center. Nucleic Acids Res. 2007; 35(Database issue):401\u20136. \n                    https:\/\/doi.org\/10.1093\/nar\/gkl858\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"3068_CR3","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","volume":"176","author":"E Pasolli","year":"2019","unstructured":"Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019; 176:649\u2013662.e20. \n                    https:\/\/doi.org\/10.1016\/j.cell.2019.01.001\n                    \n                  .","journal-title":"Cell"},{"key":"3068_CR4","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.7717\/peerj.1319","volume":"3","author":"AM Eren","year":"2015","unstructured":"Eren AM, Esen \u00d6C, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO, van Gulik W. Anvi\u2019o: an advanced analysis and visualization platform for \u2018omics data. PeerJ. 2015; 3:1319. \n                    https:\/\/doi.org\/10.7717\/peerj.1319\n                    \n                  .","journal-title":"PeerJ"},{"issue":"19","key":"3068_CR5","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"EV Kriventseva","year":"2015","unstructured":"Kriventseva EV, Zdobnov EM, Sim\u00e3o FA, Ioannidis P, Waterhouse RM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210\u20132. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btv351\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"7","key":"3068_CR6","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015; 25(7):1043\u201355.","journal-title":"Genome Res"},{"key":"3068_CR7","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.7717\/peerj.1165","volume":"3","author":"DD Kang","year":"2015","unstructured":"Kang DD, Froula J, Egan R, Wang Z. Metabat, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015; 3:1165. \n                    https:\/\/doi.org\/10.7717\/peerj.1165\n                    \n                  .","journal-title":"PeerJ"},{"key":"3068_CR8","doi-asserted-by":"publisher","first-page":"8365; 8365","DOI":"10.1038\/srep08365","volume":"5","author":"T Brettin","year":"2015","unstructured":"Brettin T, Davis JJ, Disz T, Edwards R, Gerdes S, Olsen G, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason 3rd JA, Stevens R, Vonstein V, Wattam AR, Xia F. Rasttk: a modular and extensible implementation of the rast algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365; 8365\u20138365. \n                    https:\/\/doi.org\/10.1038\/srep08365\n                    \n                  .","journal-title":"Sci Rep"},{"issue":"17","key":"3068_CR9","doi-asserted-by":"publisher","first-page":"5691","DOI":"10.1093\/nar\/gki866","volume":"33","author":"R Overbeek","year":"2005","unstructured":"Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Cr\u00e9cy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, R\u00fcckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33(17):5691\u2013702. \n                    https:\/\/doi.org\/10.1093\/nar\/gki866\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"3068_CR10","doi-asserted-by":"crossref","unstructured":"Weisstein EW. CRC Concise Encyclopedia of Mathematics: CRC Press; 2002.","DOI":"10.1201\/9781420035223"},{"issue":"Database issue","key":"3068_CR11","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1093\/nar\/gkt1226","volume":"42","author":"R Overbeek","year":"2014","unstructured":"Overbeek R, Olson R, Pusch GD, Olsen G, Davis JJ, Disz T, Edwards R, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. The seed and the rapid annotation of microbial genomes using subsystems technology (rast). Nucleic Acids Res. 2014; 42(Database issue):206\u201314. \n                    https:\/\/doi.org\/10.1093\/nar\/gkt1226\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"3068_CR12","unstructured":"Genome Annotation. \n                    https:\/\/docs.patricbrc.org\/tutorial\/genome_annotation\/annotation.html\n                    \n                  . Accessed 01 Sept 2019."},{"key":"3068_CR13","unstructured":"Comprehensive Genome Analysis Service. \n                    https:\/\/docs.patricbrc.org\/tutorial\/comprehensive-genome-analysis\/comprehensive-genome-analysis.html\n                    \n                  . Accessed 01 Sept 2019."},{"key":"3068_CR14","unstructured":"Using the PATRIC Metagenomic Binning Service. \n                    https:\/\/docs.patricbrc.org\/tutorial\/metagenomic_binning\/metagenomic_binning.html\n                    \n                  . 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Accessed 01 Sept 2019."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3068-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-3068-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3068-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T23:16:40Z","timestamp":1601594200000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3068-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,3]]},"references-count":15,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["3068"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-3068-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,3]]},"assertion":[{"value":"1 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 October 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"486"}}