{"id":22301340,"url":"https://github.com/claczny/busybee_web","last_synced_at":"2026-01-06T02:40:07.051Z","repository":{"id":150544402,"uuid":"88028029","full_name":"claczny/busybee_web","owner":"claczny","description":"Repository for BusyBee Web - Web-based deconvolution of metagenomic data by bootstrapped supervised binning","archived":false,"fork":false,"pushed_at":"2017-05-03T08:38:59.000Z","size":1082,"stargazers_count":2,"open_issues_count":4,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-30T20:44:47.574Z","etag":null,"topics":["binning","metagenomics","unsupervised-learning","website"],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/claczny.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-04-12T08:25:40.000Z","updated_at":"2018-03-21T16:51:52.000Z","dependencies_parsed_at":"2023-05-01T17:54:13.986Z","dependency_job_id":null,"html_url":"https://github.com/claczny/busybee_web","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/claczny%2Fbusybee_web","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/claczny%2Fbusybee_web/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/claczny%2Fbusybee_web/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/claczny%2Fbusybee_web/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/claczny","download_url":"https://codeload.github.com/claczny/busybee_web/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245563032,"owners_count":20635907,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["binning","metagenomics","unsupervised-learning","website"],"created_at":"2024-12-03T18:19:54.001Z","updated_at":"2026-01-06T02:40:02.016Z","avatar_url":"https://github.com/claczny.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;![BusyBee Web - metagenomic data analysis by bootstrapped supervised binning and annotation](images/Busybee_web_on_right_side_medium_size_low_res.png)\n\nBusyBee Web (https://ccb-microbe.cs.uni-saarland.de/busybee/) is a web-based, automated, and reference-independent binning tool for metagenomic data in the form of **assembled contigs** or **long reads** (PacBio, Oxford Nanopore Technologies).\n\n**No installation** is required; simply upload your FASTA file and give it a go.\nBusyBee Web is based on concepts developed in the context of [VizBin](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-014-0066-1) and thus tries to combine [automated clustering and human inspection](https://www.nature.com/articles/nmicrobiol2016180) into a user-friendly web application.\nMoreover, bin quality estimates are provided as complementary means to the visual inspection.\nYou can optionally enable **taxonomic** annotation using Kraken and the Minikraken database, as well as let BusyBee Web annotate *putative* **antibiotic resistance genes**.\nTaxonomic annotation is quick, the functional annotation may take a bit though as genes have to be called first, etc.\n\n## DEMO\n\n[Demo results - 2D scatterplot](images/results.scatterplot_abx.png)\n\n[Demo results - Bin quality estimates table](images/results.bin_quality_table.png)\n\n[Demo results - Taxonomic composition comparison](images/results.taxonomic_composition_compared.png)\n\n# PUBLICATION\nGreat news!!! The paper is now out at *Nucleic Acids Research* (https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx348).\n\nIf you use BusyBee Web, please cite it as\n\n\u003e Cedric C. Laczny, Christina Kiefer, Valentina Galata, Tobias Fehlmann, Christina Backes, Andreas Keller; BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. *Nucleic Acids Res* 2017 gkx348. doi: 10.1093/nar/gkx348\n\nAlternatively, as soon as this is working from the publisher's side - BusyBee Web is fresh-from-the-oven -, you can format your citation via https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx348 -\u003e \"Cite\", e.g., [BibTex](https://academic.oup.com/nar/downloadcitation/3787850?format=bibtex) or [EndNote](https://academic.oup.com/nar/downloadcitation/3787850?format=ris).\n\n# ISSUES\nWhile the web server is principally stable, we are actively working on extending BusyBee Web's functionality.\nMoreover, we are curious to see what the load on the server will be.\n\nIn any case, you can contact Cedric via his Twitter handle **@claczny**.\n\nShould the service be unavailable or should you find that your jobs are waiting in the queue for some time, we would greatly appreciate if you could let us know so we can adjust the hardware requirements accordingly.\nPlease open a [new issue](https://github.com/claczny/busybee_web/issues/new) in that case.\n\nShould you run into any other issues when using BusyBee Web, please post [an issue](https://github.com/claczny/busybee_web/issues/new) and we will get back to you ASAP.\n\n# TUTORIAL \u0026 F.A.Q.s\nWe provide a [step-by-step tutorial](https://ccb-microbe.cs.uni-saarland.de/busybee/tutorial/) and [F.A.Q.s](https://ccb-microbe.cs.uni-saarland.de/busybee/fqa/).\n\nShould you have questions which are not answered there, just let us know.\nA good way to do this is to open a [new issue](https://github.com/claczny/busybee_web/issues/new) describing your question.\n\n# DISCLAIMER\nTHIS SOFTWARE IS PROVIDED BY THE CHAIR FOR CLINICAL BIOINFORMATICS (SAARLAND UNIVERSITY) AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE CHAIR FOR CLINICAL BIOINFORMATICS (SAARLAND UNIVERSITY) OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \n\nSee also the [About \u0026 Disclaimer page](https://ccb-microbe.cs.uni-saarland.de/busybee/about/).\n\n# LOGO\nThe logo was designed by the hyper-talented Linda Wampach (Twitter: **@wampachl**).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclaczny%2Fbusybee_web","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fclaczny%2Fbusybee_web","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fclaczny%2Fbusybee_web/lists"}