{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T16:57:53Z","timestamp":1776704273593,"version":"3.51.2"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,14]],"date-time":"2022-10-14T00:00:00Z","timestamp":1665705600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001866","name":"National Research Fund","doi-asserted-by":"publisher","award":["PRIDE\/11823097"],"award-info":[{"award-number":["PRIDE\/11823097"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-CoG 863664"],"award-info":[{"award-number":["ERC-CoG 863664"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete ($\\gt 95\\%$ pure, $\\gt 90\\%$ complete) and high-quality ($\\gt 90\\%$ pure, $\\gt 70\\%$ complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.<\/jats:p>","DOI":"10.1093\/bib\/bbac431","type":"journal-article","created":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T16:49:59Z","timestamp":1662569399000},"source":"Crossref","is-referenced-by-count":23,"title":["<i>binny<\/i>\n                    : an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9959-8767","authenticated-orcid":false,"given":"Oskar","family":"Hickl","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0831-4261","authenticated-orcid":false,"given":"Pedro","family":"Queir\u00f3s","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6478-2924","authenticated-orcid":false,"given":"Paul","family":"Wilmes","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8698-3770","authenticated-orcid":false,"given":"Patrick","family":"May","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9780-1933","authenticated-orcid":false,"given":"Anna","family":"Heintz-Buschart","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2022,10,13]]},"reference":[{"issue":"9","key":"2022112111121711200_ref1","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nbt.3935","article-title":"Shotgun 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