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datasets","url":"http://creativecommons.org/licenses/by-nd/4.0/"}],"citation":{"@type":"ScholarlyArticle","@id":"https://doi.org/10.1093/molbev/msab199","name":"BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.","author":[{"@type":"Person","givenName":"Mosè","familyName":"Manni"},{"@type":"Person","givenName":"Matthew R","familyName":"Berkeley"},{"@type":"Person","givenName":"Mathieu","familyName":"Seppey"},{"@type":"Person","givenName":"Felipe A","familyName":"Simão"},{"@type":"Person","givenName":"Evgeny M","familyName":"Zdobnov","identifier":"https://orcid.org/0000-0002-5178-1498"}],"url":"https://pubmed.ncbi.nlm.nih.gov/pubmed/34320186"},"provider":[{"@type":"Organization","name":"University of Geneva","sameAs":"https://ror.org/01swzsf04","url":"https://www.unige.ch/"},{"@type":"Organization","name":"SIB Swiss Institute of 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class="hero"><img src="/home/busco.png" alt="hero">  <p class="description"> from QC to gene prediction and phylogenomics </p> </header>  <div class="theme-default-content custom content__default"><div class="tip custom-block"><p><strong>BUSCO v5.8.1 is the current stable version!</strong><br> <a href="https://gitlab.com/ezlab/busco/-/releases#5.8.1" target="_blank" rel="noopener noreferrer">Gitlab<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, a <a href="https://anaconda.org/bioconda/busco" target="_blank" rel="noopener noreferrer">Conda package<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> and <a href="https://hub.docker.com/r/ezlabgva/busco/tags?page=1&ordering=last_updated" target="_blank" rel="noopener noreferrer">Docker container<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> are also available.</p></div> <div class="tip custom-block"><p>Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, the BUSCO metric is complementary to technical metrics like N50.</p></div> <div class="tip custom-block"><p><strong>BUSCO was selected as one of the <a href="https://www.sib.swiss/about-sib/news/10904-sib-remarkable-outputs-2021" target="_blank" rel="noopener noreferrer">SIB Remarkable Outputs of 2021<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>!</strong></p></div> <h2 id="cite-us"><a href="#cite-us" aria-hidden="true" class="header-anchor">#</a> Cite us</h2> <p>The latest BUSCO paper, describing the novelties introduced in BUSCO v4 and v5 and the new BUSCO datasets (*_odb10) are described <a href="https://academic.oup.com/mbe/article/38/10/4647/6329644" target="_blank" rel="noopener noreferrer">here<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>. If you've used these versions or datasets the correct citation would be:<br> <br> <em>Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov, <a href="https://academic.oup.com/mbe/article/38/10/4647/6329644" target="_blank" rel="noopener noreferrer"><strong>BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes</strong>.<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654</em></p> <p>The following protocol covers the various BUSCO running modes and workflows, BUSCO setup, guidelines to interpret the results, and additional analyses, e.g., for building phylogenomic trees and visualizing syntenies using BUSCO results:<br> <br> <em>Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.323" target="_blank" rel="noopener noreferrer"><strong>BUSCO: Assessing genomic data quality and beyond.</strong><svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> Current Protocols, 1, e323. doi: 10.1002/cpz1.323</em></p> <a href="https://scholar.google.ch/citations?user=WbkbmUEAAAAJ" target="_blank" rel="noopener noreferrer" class="custom navbutton"> more & stats >> <svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> <h2 id="license"><a href="#license" aria-hidden="true" class="header-anchor">#</a> License</h2> <p>The BUSCO software is licensed under the MIT License.</p> <p>The BUSCO datasets are licensed under the Creative Commons Attribution-NoDerivatives 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nd/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p> <p>Any use of these datasets for analyses in a publication or product must include the citation of the corresponding paper: <a href="https://doi.org/10.1093/molbev/msab199" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/molbev/msab199<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>.</p> <h2 id="obtain-busco"><a href="#obtain-busco" aria-hidden="true" class="header-anchor">#</a> Obtain BUSCO</h2> <p>Full installation instructions are provided in the <a href='/busco_userguide'>user guide</a> and <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.323" target="_blank" rel="noopener noreferrer">protocols<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>.</p> <p>BUSCO is available as a conda package and as a Docker image. Both of these versions are ready to run out of the box. Alternatively, it is also possible to manually install BUSCO.</p> <p>The BUSCO software directly downloads the necessary datasets, whether they are specified by the user or automatically selected by BUSCO.</p> <p>To display all available datasets</p> <div class="language- extra-class"><pre class="language-text"><code>busco --list-datasets </code></pre></div><p>You can also download them <a href="https://busco-data.ezlab.org/v5/data/lineages/" target="_blank" rel="noopener noreferrer">manually<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>.</p> <p>Earlier versions: <a href="https://gitlab.com/ezlab/busco/-/releases#4.1.4" target="_blank" rel="noopener noreferrer">v4<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="http://busco.ezlab.org/v3" target="_blank" rel="noopener noreferrer">v3<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="http://busco.ezlab.org/v2" target="_blank" rel="noopener noreferrer">v2<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="http://busco.ezlab.org/v1" target="_blank" rel="noopener noreferrer">v1<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></p> <h2 id="documentation-and-support"><a href="#documentation-and-support" aria-hidden="true" class="header-anchor">#</a> Documentation and support</h2> <a class='custom navbutton' href='/busco_userguide' rel='noopener noreferrer' target='_blank'> User guide <svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> <a href="https://gitlab.com/ezlab/busco/issues" target="_blank" rel="noopener noreferrer" class="custom navbutton"> Issues board <svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> <h2 id="core-genes"><a href="#core-genes" aria-hidden="true" class="header-anchor">#</a> "Core" genes</h2> <p><a href="https://doi.org/10.1093/gbe/evq083" target="_blank" rel="noopener noreferrer"><img src="/home/busco_sampling.png" alt="BUSCO sampling space"> adapted from<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></p> <p><div class="s-footer-box"><div class="s-footer"><div class="footer-left s-nav-logos"><a href="https://www.ezlab.org/" target="_blank">EZ<em>lab</em></a> <a href="https://www.orthodb.org/" target="_blank">Ortho<em>DB</em></a> <a href="https://lemortho.ezlab.org/" target="_blank">LEM<em>Ortho</em></a> <a href="https://lemmi.ezlab.org/" target="_blank">LEM<em>MI</em></a> <a href="https://lemmi16s.ezlab.org/" target="_blank">LEM<em>MI16s</em></a> <a href="https://mirmap.ezlab.org/" target="_blank">miR<em>map</em></a> <a href="http://www.ezlab.org/#newick-utils" target="_blank">Newick<em>Utils</em></a></div> <div class="footer-right"> © 2019 EM Zdobnov Group - <a href="https://www.unige.ch/medecine/gede/en/research-groups/830zdobnov/">UNIGE</a> / <a href="https://www.sib.swiss/evgeny-zdobnov-group">SIB</a></div></div></div></p></div> </main></div><div class="global-ui"></div></div> <script src="/assets/js/app.451a7927.js" defer></script><script src="/assets/js/2.9b61b5f0.js" defer></script><script src="/assets/js/9.9013cdfc.js" defer></script><script src="/assets/js/12.2533d619.js" defer></script><script src="/assets/js/4.af2e188d.js" defer></script><script src="/assets/js/3.b22d9d47.js" defer></script> </body> </html>