{"id":13737121,"url":"https://github.com/ababaian/serratus","last_synced_at":"2025-04-07T06:05:21.039Z","repository":{"id":37431648,"uuid":"244498848","full_name":"ababaian/serratus","owner":"ababaian","description":"Ultra-deep search for novel viruses","archived":false,"fork":false,"pushed_at":"2023-03-29T17:16:28.000Z","size":7209,"stargazers_count":267,"open_issues_count":39,"forks_count":34,"subscribers_count":18,"default_branch":"master","last_synced_at":"2025-03-31T05:02:49.893Z","etag":null,"topics":["aws","bioinformatics","coronavirus","covid19","open-science","sars-cov-2"],"latest_commit_sha":null,"homepage":"http://serratus.io","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ababaian.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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}},"created_at":"2020-03-02T23:38:02.000Z","updated_at":"2025-03-14T14:14:29.000Z","dependencies_parsed_at":"2024-01-06T14:52:28.417Z","dependency_job_id":null,"html_url":"https://github.com/ababaian/serratus","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ababaian%2Fserratus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ababaian%2Fserratus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ababaian%2Fserratus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ababaian%2Fserratus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ababaian","download_url":"https://codeload.github.com/ababaian/serratus/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247601447,"owners_count":20964864,"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":["aws","bioinformatics","coronavirus","covid19","open-science","sars-cov-2"],"created_at":"2024-08-03T03:01:35.576Z","updated_at":"2025-04-07T06:05:21.012Z","avatar_url":"https://github.com/ababaian.png","language":"Jupyter Notebook","funding_links":[],"categories":["Jupyter Notebook"],"sub_categories":[],"readme":"# Serratus\n\nSerratus is a collaborative Open Science project for ultra-rapid discovery of all viruses.\n\n#### Paper: [Petabase-scale sequence alignment catalyses viral discovery](https://www.nature.com/articles/s41586-021-04332-2)\n\n[![Serratus Mountain in Squamish, BC. Canada](https://github.com/ababaian/serratus/wiki/img/splash.png)](https://www.biorxiv.org/content/10.1101/2020.08.07.241729v1)\n\n### Background\n\n_Forewarned is Forearmed._\n\nOur primary goal is to generate the viral data to accelerate the global research efforts in fighting emerging pathogens. We are re-analyzing all RNA-seq, meta-genomics, meta-transcriptomics and environmental sequencing data in the NCBI Short Read Archive to discover new viruses. That is **\u003e6 million biological samples** or \u003e10 petabases of sequencing data.\n\n### Contribute to Serratus\nThe `Serratus` team is actively looking to collaborate with all scientists and developers.\n\n- See: [CONTRIBUTING.md](CONTRIBUTING.md)\n- Join the [`Serratus Slack`](mailto:artem@rRNA.ca?subject=Joining%20the%20Serratus%20slack\u0026body=Hello%20I%20would%20like%20to%20join%20the%20Serratus%20chat.%20Thanks!) to chat / ask a question.\n\n# Serratus Usage\nLearn more on the [Serratus Wiki](https://github.com/ababaian/serratus/wiki/)\n\n### [Serratus Data Explorer](https://serratus.io)\n\n### [palmID: RdRP search](https://serratus.io/palmid)\n\n### [How To: Finding Novel Viruses](https://github.com/ababaian/serratus/wiki/Find_novel_viruses)\n\n### [Accessing Raw Data](https://github.com/ababaian/serratus/wiki/Access-Data-Release) \n\n### [Cloud Architecture](https://github.com/ababaian/serratus/wiki/Architecture-and-Pipeline)\n\n### [Serratus CLI Usage](https://github.com/ababaian/serratus/wiki/Running-Serratus)\n\n# Data Release Policy\n\nOur primary goal is to generate the viral data to accelerate the global research efforts in fighting emerging pathogens. To achieve this:\n\n- All software development is open-source and freely available (GPLv3)\n\n- All data, raw and processed, will be freely and immediatly available in the public domain in accordance with the [INSDC Policy](https://www.insdc.org/policy/).\n\n---\n\n## [About The Team](CONTRIBUTORS.md)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fababaian%2Fserratus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fababaian%2Fserratus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fababaian%2Fserratus/lists"}