{"id":21679076,"url":"https://github.com/colinbrislawn/unite-train","last_synced_at":"2026-04-05T22:08:25.034Z","repository":{"id":70708810,"uuid":"448594227","full_name":"colinbrislawn/unite-train","owner":"colinbrislawn","description":"🍄 Qiime2 ITS classifiers for the UNITE database","archived":false,"fork":false,"pushed_at":"2025-03-16T17:25:50.000Z","size":1082,"stargazers_count":36,"open_issues_count":0,"forks_count":5,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-16T18:54:10.144Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/colinbrislawn.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-01-16T15:29:58.000Z","updated_at":"2025-03-16T17:25:54.000Z","dependencies_parsed_at":"2023-11-07T03:08:47.383Z","dependency_job_id":"975a5bb2-2f16-47ec-9aca-4e8b04b3dee5","html_url":"https://github.com/colinbrislawn/unite-train","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/colinbrislawn/unite-train","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/colinbrislawn%2Funite-train","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/colinbrislawn%2Funite-train/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/colinbrislawn%2Funite-train/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/colinbrislawn%2Funite-train/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/colinbrislawn","download_url":"https://codeload.github.com/colinbrislawn/unite-train/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/colinbrislawn%2Funite-train/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29062480,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T23:14:54.203Z","status":"ssl_error","status_checked_at":"2026-02-03T23:14:50.873Z","response_time":96,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2024-11-25T14:48:18.498Z","updated_at":"2026-02-04T00:00:20.030Z","avatar_url":"https://github.com/colinbrislawn.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# unite-train\n\nA pipeline to build [Qiime2](https://qiime2.org/) taxonomy [classifiers](https://docs.qiime2.org/2021.11/data-resources/) for the [UNITE database](https://unite.ut.ee/repository.php).\n\n## [Download a pre-trained classifier here! 🎁](https://github.com/colinbrislawn/unite-train/releases)\n\n[![Issues](https://img.shields.io/github/issues/colinbrislawn/unite-train?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/issues)\n![pre-releases](https://img.shields.io/github/release-date-pre/colinbrislawn/unite-train?display_date=published_at\u0026style=for-the-badge)\n[![Downloads](https://img.shields.io/github/downloads/colinbrislawn/unite-train/total.svg?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/releases)\n\n### What is this?\n\nIf you are interested in Fungi 🍄🍄‍🟫 you could use their genomic fingerprint to identify them. Affordable PCR amplification and sequencing of the ITS gene gives you these nucleic acid fingerprints, and the UNITE team provides a database to gives these sequences a name.\n\nWe can predict the taxonomy of our fungal fingerprints using an old-school machine learning method: a supervised [k-mer](https://en.wikipedia.org/wiki/K-mer) [nb-classifier](https://scikit-learn.org/stable/modules/naive_bayes.html). But first, we need to prepare our database in a process called 'training.'\n\nThis is a pipeline that trains the UNITE ITS taxonomy database for use with Qiime2. You can run this pipeline yourself, but you don't have to! I've provided a [ready to use pre-trained classifiers](https://github.com/colinbrislawn/unite-train/releases) so you can simply run [`qiime feature-classifier classify-sklearn`](https://docs.qiime2.org/2024.2/plugins/available/feature-classifier/classify-sklearn/).\n\nIf you have questions about using Qiime2, ask on [the Qiime2 forums](https://forum.qiime2.org/).\n\nIf you have questions about the UNITE ITS database, [contact the UNITE team](https://unite.ut.ee/contact.php).\n\nIf you have questions about this pipeline, please [open a new issue](https://github.com/colinbrislawn/unite-train/issues/new)!\n\n---\n\n## Running Nextflow Workflow\n\nSet up:\n\n- Install [qiime2-amplicon with conda](https://library.qiime2.org/quickstart/amplicon)\n- Install [Nextflow with conda](https://www.nextflow.io/docs/latest/install.html#conda)\n\nConfigure \u0026 Run:\n\n```sh\n# edit config as needed (update path to qiime2 conda env)\nopen nextflow.config\n\n# Run nextflow: All save report to ./results/\nexport NXF_OFFLINE=TRUE\nnextflow run main.nf -resume\n```\n\n## Downloads\n\n![Downloads Time](./benchmarks/downloads_time.png)\n\n![Downloads Types](./benchmarks/downloads_types.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcolinbrislawn%2Funite-train","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcolinbrislawn%2Funite-train","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcolinbrislawn%2Funite-train/lists"}