{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T12:11:35Z","timestamp":1769515895022,"version":"3.49.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,4,30]],"date-time":"2022-04-30T00:00:00Z","timestamp":1651276800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005690","name":"Saarland University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005690","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https:\/\/www.ccb.uni-saarland.de\/busybee.<\/jats:p>","DOI":"10.1093\/nar\/gkac298","type":"journal-article","created":{"date-parts":[[2022,4,15]],"date-time":"2022-04-15T04:00:25Z","timestamp":1649995225000},"page":"W132-W137","source":"Crossref","is-referenced-by-count":14,"title":["BusyBee Web: towards comprehensive and differential composition-based metagenomic binning"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9627-9223","authenticated-orcid":false,"given":"Georges P","family":"Schmartz","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Pascal","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"}]},{"given":"J\u00e9r\u00e9my","family":"Amand","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Jan","family":"Dastbaz","sequence":"additional","affiliation":[{"name":"Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"},{"name":"Deutsches Zentrum f\u00fcr Infektionsforschung (DZIF) , Standort Hannover-Braunschweig, 38124 Braunschweig , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1967-2918","authenticated-orcid":false,"given":"Tobias","family":"Fehlmann","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8223-3750","authenticated-orcid":false,"given":"Fabian","family":"Kern","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Rolf","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"},{"name":"Deutsches Zentrum f\u00fcr Infektionsforschung (DZIF) , Standort Hannover-Braunschweig, 38124 Braunschweig , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research , 66123 Saarbr\u00fccken, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,4,30]]},"reference":[{"key":"2022070423581105700_B1","doi-asserted-by":"crossref","first-page":"e65088","DOI":"10.7554\/eLife.65088","article-title":"Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3","volume":"10","author":"Beghini","year":"2021","journal-title":"Elife"},{"key":"2022070423581105700_B2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"2022070423581105700_B3","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbz155","article-title":"Current challenges and best-practice protocols for microbiome analysis","volume":"22","author":"Bharti","year":"2021","journal-title":"Brief. 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