{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T10:28:21Z","timestamp":1774693701878,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T00:00:00Z","timestamp":1566518400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2017-03709"],"award-info":[{"award-number":["2017-03709"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Carl Tryggers Foundation","award":["CTS 15:184"],"award-info":[{"award-number":["CTS 15:184"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence\/absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence\/absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>miComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https:\/\/bitbucket.org\/evolegiolab\/micomplete.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz664","type":"journal-article","created":{"date-parts":[[2019,8,20]],"date-time":"2019-08-20T19:16:59Z","timestamp":1566328619000},"page":"936-937","source":"Crossref","is-referenced-by-count":43,"title":["miComplete: weighted quality evaluation of assembled microbial genomes"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0819-3359","authenticated-orcid":false,"given":"Eric","family":"Hugoson","sequence":"first","affiliation":[{"name":"Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University , Uppsala SE-751 23, Sweden"},{"name":"Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology , Pl\u00f6n D-24306, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0098-1692","authenticated-orcid":false,"given":"Wai Tin","family":"Lam","sequence":"additional","affiliation":[{"name":"Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology , Pl\u00f6n D-24306, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8354-2398","authenticated-orcid":false,"given":"Lionel","family":"Guy","sequence":"additional","affiliation":[{"name":"Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University , Uppsala SE-751 23, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2019,8,22]]},"reference":[{"key":"2023013110075726200_btz664-B1","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013110075726200_btz664-B2","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1093\/bioinformatics\/btw824","article-title":"phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics","volume":"33","author":"Guy","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013110075726200_btz664-B3","doi-asserted-by":"crossref","first-page":"119.","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023013110075726200_btz664-B12","doi-asserted-by":"crossref","first-page":"e1001177","DOI":"10.1371\/journal.pbio.1001177","article-title":"A holistic approach to marine eco-systems biology","volume":"9","author":"Karsenti","year":"2011","journal-title":"PLOS Biol"},{"key":"2023013110075726200_btz664-B4","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/S0968-0004(00)01663-7","article-title":"Gene context conservation of a higher order than operons","volume":"25","author":"Lathe","year":"2000","journal-title":"Trends Biochem. 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