{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T23:25:04Z","timestamp":1776381904110,"version":"3.51.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,10,20]],"date-time":"2022-10-20T00:00:00Z","timestamp":1666224000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Collaborative Research Center 1182: Origin and Function of Metaorganisms","award":["SFB 1182"],"award-info":[{"award-number":["SFB 1182"]}]},{"name":"Collaborative Research Center 1182: Origin and Function of Metaorganisms","award":["261376515"],"award-info":[{"award-number":["261376515"]}]},{"name":"DFG Research Unit 5042"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic data is an important task for the comprehensive analysis of microbial communities from variable sources. Single binning tools differ in their ability to leverage specific aspects in MAG reconstruction, the use of ensemble binning refinement tools is often time consuming and computational demand increases with community complexity. We introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality MAGs from the output of multiple genome-binning tools.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>MAGScoT is available via GitHub (https:\/\/github.com\/ikmb\/MAGScoT) and as an easy-to-use Docker container (https:\/\/hub.docker.com\/repository\/docker\/ikmb\/magscot).<\/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\/btac694","type":"journal-article","created":{"date-parts":[[2022,10,19]],"date-time":"2022-10-19T12:53:00Z","timestamp":1666183980000},"page":"5430-5433","source":"Crossref","is-referenced-by-count":51,"title":["<tt>MAGScoT<\/tt>: a fast, lightweight and accurate bin-refinement tool"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0685-0052","authenticated-orcid":false,"given":"Malte Christoph","family":"R\u00fchlemann","sequence":"first","affiliation":[{"name":"Institute of Clinical Molecular Biology, Kiel University , 24105 Kiel, Germany"},{"name":"Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School , 30625 Hannover, Germany"}]},{"given":"Eike Matthias","family":"Wacker","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Kiel University , 24105 Kiel, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4332-6110","authenticated-orcid":false,"given":"David","family":"Ellinghaus","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Kiel University , 24105 Kiel, Germany"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Kiel University , 24105 Kiel, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,10,20]]},"reference":[{"key":"2022121418373800500_btac694-B1","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41586-019-0965-1","article-title":"A new genomic blueprint of the human gut microbiota","volume":"568","author":"Almeida","year":"2019","journal-title":"Nature"},{"key":"2022121418373800500_btac694-B2","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. Methods"},{"key":"2022121418373800500_btac694-B3","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"2022121418373800500_btac694-B4","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":"2022121418373800500_btac694-B5","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1186\/1471-2105-11-431","article-title":"Hidden Markov model speed heuristic and iterative HMM search procedure","volume":"11","author":"Johnson","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2022121418373800500_btac694-B6","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"2022121418373800500_btac694-B7","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"2022121418373800500_btac694-B8","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/s41592-022-01431-4","article-title":"Critical assessment of metagenome interpretation: the second round of challenges","volume":"19","author":"Meyer","year":"2022","journal-title":"Nat. Methods"},{"key":"2022121418373800500_btac694-B9","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.1093\/nar\/gkt263","article-title":"Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions","volume":"41","author":"Mistry","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022121418373800500_btac694-B10","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41587-020-00777-4","article-title":"Improved metagenome binning and assembly using deep variational autoencoders","volume":"39","author":"Nissen","year":"2021","journal-title":"Nat. Biotechnol"},{"key":"2022121418373800500_btac694-B11","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"2022121418373800500_btac694-B12","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"2022121418373800500_btac694-B13","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","article-title":"Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy","volume":"3","author":"Sieber","year":"2018","journal-title":"Nat. Microbiol"},{"key":"2022121418373800500_btac694-B14","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"2022121418373800500_btac694-B15","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinform. Oxf. Engl"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac694\/46780172\/btac694.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/24\/5430\/47886922\/btac694.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/24\/5430\/47886922\/btac694.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T04:02:15Z","timestamp":1701230535000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/24\/5430\/6764585"}},"subtitle":[],"editor":[{"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,10,20]]},"references-count":15,"journal-issue":{"issue":"24","published-online":{"date-parts":[[2022,10,20]]},"published-print":{"date-parts":[[2022,12,13]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac694","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,12,15]]},"published":{"date-parts":[[2022,10,20]]}}}