{"id":9404,"name":"autometa","description":"Autometa: Automated Extraction of Genomes from Shotgun Metagenomes","url":"https://github.com/kwanlab/autometa","last_synced_at":"2025-09-04T20:29:10.955Z","repository":{"id":37799266,"uuid":"222569044","full_name":"KwanLab/Autometa","owner":"KwanLab","description":"Autometa: Automated Extraction of Genomes from Shotgun Metagenomes","archived":false,"fork":false,"pushed_at":"2025-01-24T20:14:04.000Z","size":82729,"stargazers_count":41,"open_issues_count":40,"forks_count":15,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-11T15:56:17.811Z","etag":null,"topics":["binning","metagenomics","taxon-profiling"],"latest_commit_sha":null,"homepage":"https://autometa.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KwanLab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-11-19T00:03:03.000Z","updated_at":"2025-03-11T04:27:43.000Z","dependencies_parsed_at":"2024-01-30T00:29:22.219Z","dependency_job_id":"f83a7e0d-669c-49b8-902d-88f1f5930248","html_url":"https://github.com/KwanLab/Autometa","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/KwanLab/Autometa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KwanLab","download_url":"https://codeload.github.com/KwanLab/Autometa/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273668036,"owners_count":25146690,"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","status":"online","status_checked_at":"2025-09-04T02:00:08.968Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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"}},"owner":{"login":"KwanLab","name":"KwanLab","uuid":"10067254","kind":"organization","description":"https://twitter.com/kwan_lab","email":null,"website":"kwanlab.github.io","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/10067254?v=4","repositories_count":3,"last_synced_at":"2023-03-05T20:53:50.040Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/KwanLab","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-15T22:41:41.504Z","updated_at":"2023-03-05T20:53:50.051Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KwanLab","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KwanLab/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"KwanLab/Autometa","html_url":"https://github.com/KwanLab/Autometa","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-31T23:35:44.233Z","updated_at":"2025-09-03T04:04:51.809Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/KwanLab%2FAutometa/issues","issue_labels_count":{"bug":2,"hotfix":1,"continuous integration":1,"good first issue":1,"python":1,"deprecation":1},"pull_request_labels_count":{"bug":4,"hotfix":1,"enhancement":1},"issue_author_associations_count":{"NONE":3,"CONTRIBUTOR":3,"MEMBER":1,"COLLABORATOR":1},"pull_request_author_associations_count":{"MEMBER":7,"COLLABORATOR":5},"issue_authors":{"hyphaltip":3,"imonteroo":2,"chasemc":1,"bindiyabajracharya":1,"evanroyrees":1},"pull_request_authors":{"chasemc":7,"Sidduppal":4,"shaneroesemann":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10081055,"issues_count":31277800,"pull_requests_count":96105963,"authors_count":10693660,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":1},"past_year_pull_request_author_associations_count":{"MEMBER":4},"past_year_issue_authors":{"chasemc":1},"past_year_pull_request_authors":{"chasemc":4},"maintainers":[{"login":"chasemc","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/chasemc"},{"login":"Sidduppal","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Sidduppal"},{"login":"shaneroesemann","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/shaneroesemann"},{"login":"evanroyrees","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/evanroyrees"}],"active_maintainers":[{"login":"chasemc","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/chasemc"}]},"events":{"total":{"IssuesEvent":1,"WatchEvent":4,"DeleteEvent":2,"IssueCommentEvent":32,"PushEvent":37,"PullRequestReviewEvent":2,"PullRequestEvent":8,"CreateEvent":4},"last_year":{"IssuesEvent":1,"WatchEvent":4,"DeleteEvent":2,"IssueCommentEvent":32,"PushEvent":37,"PullRequestReviewEvent":2,"PullRequestEvent":8,"CreateEvent":4}},"keywords":["binning","metagenomics","taxon-profiling"],"dependencies":[{"ecosystem":"pypi","filepath":"docs/requirements.txt","sha":null,"kind":"manifest","created_at":"2022-06-23T15:20:50.152Z","updated_at":"2022-06-23T15:20:50.152Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/docs/requirements.txt","dependencies":[{"id":22223191,"package_name":"sphinx","ecosystem":"pypi","requirements":"==4.2.0","direct":true,"kind":"runtime","optional":false},{"id":22223192,"package_name":"sphinx_rtd_theme","ecosystem":"pypi","requirements":"==1.0.0","direct":true,"kind":"runtime","optional":false},{"id":22223193,"package_name":"readthedocs-sphinx-search","ecosystem":"pypi","requirements":"==0.1.1","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/docker_autometa.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.621Z","updated_at":"2023-01-31T14:00:43.621Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/docker_autometa.yml","dependencies":[{"id":7272779307,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779308,"package_name":"docker/setup-qemu-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779309,"package_name":"docker/setup-buildx-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779310,"package_name":"docker/metadata-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7272779311,"package_name":"docker/login-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779312,"package_name":"docker/build-push-action","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/docker_get_genomes_for_mock.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.666Z","updated_at":"2023-01-31T14:00:43.666Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/docker_get_genomes_for_mock.yml","dependencies":[{"id":7272779320,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779321,"package_name":"docker/setup-qemu-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779322,"package_name":"docker/setup-buildx-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779323,"package_name":"docker/metadata-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7272779324,"package_name":"docker/login-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779326,"package_name":"docker/build-push-action","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/docker_mock_data_reporter.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.713Z","updated_at":"2023-01-31T14:00:43.713Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/docker_mock_data_reporter.yml","dependencies":[{"id":7272779595,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779596,"package_name":"docker/setup-qemu-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779597,"package_name":"docker/setup-buildx-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779598,"package_name":"docker/metadata-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7272779599,"package_name":"docker/login-action","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779600,"package_name":"docker/build-push-action","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.730Z","updated_at":"2023-01-31T14:00:43.730Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/linting.yml","dependencies":[{"id":7272779690,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779691,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7272779692,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.812Z","updated_at":"2023-01-31T14:00:43.812Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":7272779698,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779699,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/pytest_codecov.yml","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.845Z","updated_at":"2023-01-31T14:00:43.845Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/.github/workflows/pytest_codecov.yml","dependencies":[{"id":7272779766,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779767,"package_name":"actions/cache","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779768,"package_name":"conda-incubator/setup-miniconda","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7272779769,"package_name":"codecov/codecov-action","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"docker","filepath":"Dockerfile","sha":null,"kind":"manifest","created_at":"2023-01-31T14:00:43.925Z","updated_at":"2023-01-31T14:00:43.925Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/Dockerfile","dependencies":[{"id":7272780138,"package_name":"continuumio/miniconda3","ecosystem":"docker","requirements":"latest","direct":true,"kind":"build","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/bowtie2/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-21T01:49:33.901Z","updated_at":"2023-10-21T01:49:33.901Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/modules/nf-core/modules/bowtie2/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/prodigal/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-21T01:49:33.906Z","updated_at":"2023-10-21T01:49:33.906Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/modules/nf-core/modules/prodigal/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"setup.py","sha":null,"kind":"manifest","created_at":"2023-10-21T01:49:33.914Z","updated_at":"2023-10-21T01:49:33.914Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/setup.py","dependencies":[]},{"ecosystem":"conda","filepath":"tests/environment.yml","sha":null,"kind":"manifest","created_at":"2024-01-30T00:29:07.411Z","updated_at":"2024-01-30T00:29:07.411Z","repository_link":"https://github.com/KwanLab/Autometa/blob/main/tests/environment.yml","dependencies":[{"id":15911075654,"package_name":"attrs","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911075655,"package_name":"bedtools","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911075656,"package_name":"biopython","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911075657,"package_name":"black","ecosystem":"conda","requirements":"22.3.0","direct":true,"kind":"runtime","optional":false},{"id":15911075658,"package_name":"bowtie2","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911076090,"package_name":"diamond","ecosystem":"conda","requirements":"\u003e=2.0","direct":true,"kind":"runtime","optional":false},{"id":15911076581,"package_name":"gdown","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911077156,"package_name":"hmmer","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911077811,"package_name":"numba","ecosystem":"conda","requirements":"\u003e=0.47","direct":true,"kind":"runtime","optional":false},{"id":15911077812,"package_name":"numpy","ecosystem":"conda","requirements":"\u003e=1.13","direct":true,"kind":"runtime","optional":false},{"id":15911077813,"package_name":"pandas","ecosystem":"conda","requirements":"\u003e=1.1","direct":true,"kind":"runtime","optional":false},{"id":15911077814,"package_name":"parallel","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911077952,"package_name":"pip","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911077953,"package_name":"pre_commit","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078002,"package_name":"prodigal","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078045,"package_name":"pytest","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078046,"package_name":"pytest-cov","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078047,"package_name":"pytest-html","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078072,"package_name":"pytest-repeat","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078085,"package_name":"pytest-variables","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078086,"package_name":"python-annoy","ecosystem":"conda","requirements":"\u003e=1.11","direct":true,"kind":"runtime","optional":false},{"id":15911078102,"package_name":"requests","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078103,"package_name":"rsync","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078255,"package_name":"samtools","ecosystem":"conda","requirements":"\u003e=1.11","direct":true,"kind":"runtime","optional":false},{"id":15911078259,"package_name":"scikit-bio","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078261,"package_name":"scikit-learn","ecosystem":"conda","requirements":"\u003e=1.3","direct":true,"kind":"runtime","optional":false},{"id":15911078264,"package_name":"scipy","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078266,"package_name":"sphinx","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078268,"package_name":"sphinx_rtd_theme","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078271,"package_name":"tqdm","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911078273,"package_name":"trimap","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911079474,"package_name":"tsne","ecosystem":"conda","requirements":"","direct":true,"kind":"runtime","optional":false},{"id":15911079478,"package_name":"umap-learn","ecosystem":"conda","requirements":"\u003e=0.5","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:50:31.183Z","updated_at":"2025-10-07T08:06:34.222Z","avatar_url":"https://github.com/KwanLab.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1093/nar/gkz148"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/9404","html_url":"https://science.ecosyste.ms/projects/9404","bibtex_url":"https://science.ecosyste.ms/projects/9404/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/9404/export.apalike"}