{"id":23223091,"url":"https://github.com/nextstrain/yellow-fever","last_synced_at":"2025-08-19T11:32:56.328Z","repository":{"id":70926236,"uuid":"195083812","full_name":"nextstrain/yellow-fever","owner":"nextstrain","description":null,"archived":false,"fork":false,"pushed_at":"2024-12-16T23:38:27.000Z","size":5614,"stargazers_count":0,"open_issues_count":3,"forks_count":4,"subscribers_count":13,"default_branch":"main","last_synced_at":"2024-12-17T00:34:18.565Z","etag":null,"topics":["nextstrain","pathogen"],"latest_commit_sha":null,"homepage":null,"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/nextstrain.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":"2019-07-03T15:42:49.000Z","updated_at":"2024-12-16T23:38:30.000Z","dependencies_parsed_at":"2024-05-29T20:04:31.936Z","dependency_job_id":"714f1c56-66da-40b1-8d1a-acc295143bed","html_url":"https://github.com/nextstrain/yellow-fever","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/nextstrain%2Fyellow-fever","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fyellow-fever/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fyellow-fever/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fyellow-fever/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextstrain","download_url":"https://codeload.github.com/nextstrain/yellow-fever/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230351132,"owners_count":18212790,"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":["nextstrain","pathogen"],"created_at":"2024-12-18T23:16:01.817Z","updated_at":"2024-12-18T23:16:02.416Z","avatar_url":"https://github.com/nextstrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Nextstrain repository for yellow fever virus\n\nThis repository contains three workflows for the analysis of yellow\nfever virus data:\n\n- [`ingest/`] - Download data from GenBank, clean and curate it\n- [`phylogenetic/`][] - Filter sequences, align, construct phylogeny,\n  and export for visualization\n- [`nextclade/`][] - Create nextclade datasets\n\nEach workflow directory contains a `README.md` file with more\ninformation. The results of running both workflows are publicly\nvisible at [nextstrain.org/yellow-fever][].\n\n## Installation\n\nFollow the [standard installation instructions][] for Nextstrain's\nsuite of software tools.\n\n## Quick start\n\nRun the phylogenetic workflow by executing the following commands in\nthe repository checkout, after installing `nextstrain` per the above\ninstructions:\n\n```bash\ncd phylogenetic/\nnextstrain build .\nnextstrain view .\n```\n\nFurther documentation is available at \"[Running a pathogen workflow][]\".\n\n## Working on this repository\n\nThis repository is configured to use [pre-commit][] to help\nautomatically catch common coding errors and syntax issues with\nchanges before they are committed to the repo.\n\nIf you will be writing new code or otherwise working within this\nrepository, please do the following to get started:\n\n1. install `pre-commit`, by running either `python -m pip install\n   pre-commit` or `brew install pre-commit`, depending on your\n   preferred package management solution\n2. install the local git hooks by running `pre-commit install` from\n   the root of the repository\n3. when problems are detected, correct them in your local working tree\n   before committing them.\n\nNote that these pre-commit checks are also run in a GitHub Action when\nchanges are pushed to GitHub, so correcting issues locally will\nprevent extra cycles of correction.\n\n[`ingest/`]: ./ingest\n[`phylogenetic/`]: ./phylogenetic\n[`nextclade/`]: ./nextclade\n[nextstrain.org/yellow-fever]: https://nextstrain.org/yellow-fever\n[Running a pathogen workflow]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html\n[pre-commit]: https://pre-commit.com\n[standard installation instructions]: https://docs.nextstrain.org/en/latest/install.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fyellow-fever","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextstrain%2Fyellow-fever","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fyellow-fever/lists"}