{"id":16873689,"url":"https://github.com/dfornika/ncov-db","last_synced_at":"2026-04-18T06:02:08.193Z","repository":{"id":149831119,"uuid":"398426055","full_name":"dfornika/ncov-db","owner":"dfornika","description":"Store SARS-CoV-2 genomic analysis results from ncov2019-artic-nf and ncov-tools to a sqlite DB","archived":false,"fork":false,"pushed_at":"2021-09-29T23:11:40.000Z","size":62,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-24T23:48:45.836Z","etag":null,"topics":["data-management","extract-transform-load","sars-cov-2","sqlite"],"latest_commit_sha":null,"homepage":"","language":"Python","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/dfornika.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-08-20T23:56:31.000Z","updated_at":"2021-09-29T23:11:43.000Z","dependencies_parsed_at":null,"dependency_job_id":"4edebb57-00ba-4270-a096-f237e0931fa4","html_url":"https://github.com/dfornika/ncov-db","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/dfornika%2Fncov-db","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dfornika%2Fncov-db/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dfornika%2Fncov-db/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dfornika%2Fncov-db/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dfornika","download_url":"https://codeload.github.com/dfornika/ncov-db/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244313832,"owners_count":20433011,"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":["data-management","extract-transform-load","sars-cov-2","sqlite"],"created_at":"2024-10-13T15:26:40.974Z","updated_at":"2026-04-18T06:02:08.080Z","avatar_url":"https://github.com/dfornika.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ncov-db\n\nThis tool will pull relevant output data from analysis output directories produced by [BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf) and [BCCDC-PHL/ncov-tools-nf](https://github.com/BCCDC-PHL/ncov-tools-nf), and load them into a [SQLite](https://www.sqlite.org/index.html) database.\n\nIt is designed with our specific analysis output directory structure in mind, so may not be generally applicable to other COVID analysis datasets.\n\n## Installation\n\nncov-db is pip-installable. It is recommended to create a conda environment or python virtual environment for dependency management.\n\n```\nconda create -n ncov-db python=3\nconda activate ncov-db\npip install git+https://github.com/dfornika/ncov-db.git\n```\n\n## Usage\n\n### Initialize a new database\n\nBefore loading any data, a new database must be initialized with the appropriate database schema. This is done using the `ncov-db init` command.\nThe `ncov-db init` command takes a single argument: the path to the sqlite database file to be created.\n\n```\nusage: ncov-db init [-h] --db DB\n\noptional arguments:\n  -h, --help  show this help message and exit\n  --db DB\n```\n\nExample:\n\n```\nncov-db init --db ncov.db\n```\n\n### Load data from an analyzed sequencing run into an existing database\n\nOnce a database has been initialized, new data can be loaded using the `ncov-db load-run` command. The `ncov-db load-run` command takes two arguments: the path to the analysis directory of the run\nto be loaded, and the path to the database to load the data into.\n\n```\nusage: ncov-db load-run [-h] --db DB run_dir\n\npositional arguments:\n  run_dir\n\noptional arguments:\n  -h, --help  show this help message and exit\n  --db DB\n```\n\nExample:\n\n```\nncov-db load-run --db ncov.db /path/to/analysis_by_run/210501_M01234_0123_000000000-ABC12\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfornika%2Fncov-db","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdfornika%2Fncov-db","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfornika%2Fncov-db/lists"}