{"id":23223117,"url":"https://github.com/nextstrain/rsv","last_synced_at":"2025-08-19T11:33:02.112Z","repository":{"id":62849267,"uuid":"515978443","full_name":"nextstrain/rsv","owner":"nextstrain","description":"Workflow for RSV analyses on Nextstrain.org","archived":false,"fork":false,"pushed_at":"2024-07-18T20:28:07.000Z","size":10304,"stargazers_count":6,"open_issues_count":8,"forks_count":2,"subscribers_count":13,"default_branch":"master","last_synced_at":"2024-07-19T03:19:57.849Z","etag":null,"topics":["nextstrain","pathogen"],"latest_commit_sha":null,"homepage":"https://nextstrain.org/rsv","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":"2022-07-20T12:45:02.000Z","updated_at":"2024-07-18T20:28:10.000Z","dependencies_parsed_at":"2024-04-17T10:50:39.785Z","dependency_job_id":"00784c03-8557-445d-a389-dfda0627234e","html_url":"https://github.com/nextstrain/rsv","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%2Frsv","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Frsv/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Frsv/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Frsv/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextstrain","download_url":"https://codeload.github.com/nextstrain/rsv/tar.gz/refs/heads/master","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":"2024-12-18T23:16:07.020Z","updated_at":"2024-12-18T23:16:07.744Z","avatar_url":"https://github.com/nextstrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nextstrain.org/rsv\n\nThis is the Nextstrain build for respiratory syncytial virus (RSV). Output from this build is available at nextstrain.org/rsv.\n\n## Input Data\n\nInput metadata and sequences for RSV-A and RSV-B are available via \u003chttps://data.nextstrain.org\u003e\n\n- [RSV-A sequences](https://data.nextstrain.org/files/workflows/rsv/a/sequences.fasta.xz)\n- [RSV-A metadata](https://data.nextstrain.org/files/workflows/rsv/a/metadata.tsv.gz)\n\n- [RSV-B sequences](https://data.nextstrain.org/files/workflows/rsv/b/sequences.fasta.xz)\n- [RSV-B metadata](https://data.nextstrain.org/files/workflows/rsv/b/metadata.tsv.gz)\n\nThese data are generously shared by labs around the world and deposited in NCBI genbank by the authors.\nPlease contact these labs first if you plan to publish using these data.\nRSV sequences and metadata can be downloaded in the `/ingest` folder using\n`nextstrain build --cpus 1 ingest` or `nextstrain build --cpus 1 .` if running directly from the `/ingest` directory.\n\nThe ingest pipeline is based on the Nextstrain mpox ingest workflow (\u003chttps://github.com/nextstrain/mpox/tree/master/ingest\u003e).\nRunning the ingest pipeline produces `ingest/data/{a,b}/metadata.tsv` and `ingest/data/{a,b}/sequences.fasta`.\n\n### `ingest/vendored`\n\nThis repository uses [`git subrepo`](https://github.com/ingydotnet/git-subrepo) to manage copies of ingest scripts in [`ingest/vendored`](./ingest/vendored), from [nextstrain/ingest](https://github.com/nextstrain/ingest). To pull new changes from the central ingest repository, first install `git subrepo`, then run:\n\nSee [ingest/vendored/README.md](./ingest/vendored/README.md#vendoring) for instructions on how to update the vendored scripts.\n\n## Run Analysis Pipeline\n\nThe workflow produces whole genome and G gene trees for RSV-A and RSV-B.\nTo run the workflow, use `snakemake -j4 -p --configfile config/configfile.yaml` and `nextstrain view auspice` to visualise results.\n\n## Installation\n\nFollow the standard [installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.\n\n## Data use\n\nWe gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.\n\n## Update example data\n\n[Example data](./example_data/) is used by [CI](https://github.com/nextstrain/rsv/actions/workflows/ci.yaml). It can also be used as a small subset of real-world data.\n\nExample data should be updated every time metadata schema is changed. To update, run:\n\n```sh\nnextstrain build --docker . update_example_data -F\n```\n\n\n## Sending data to the `nextclade_data` repo\n\nFrom within the destination directory, run\n```\nrsync -a \u003cpath-to\u003e/rsv/nextclade/datasets/ .\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Frsv","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextstrain%2Frsv","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Frsv/lists"}