{"id":23223102,"url":"https://github.com/nextstrain/mpox","last_synced_at":"2025-05-09T00:07:26.426Z","repository":{"id":36990761,"uuid":"493877605","full_name":"nextstrain/mpox","owner":"nextstrain","description":"Nextstrain build for mpox virus","archived":false,"fork":false,"pushed_at":"2025-05-01T20:57:57.000Z","size":34884,"stargazers_count":46,"open_issues_count":32,"forks_count":21,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-05-09T00:07:14.763Z","etag":null,"topics":["augur","auspice","bioinformatics","genbank","genomic-epidemiology","metadata","monkeypox","mpox","nextstrain","pathogen","phylogenetics","pipeline","virus-evolution"],"latest_commit_sha":null,"homepage":"https://nextstrain.org/mpox","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nextstrain.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,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-05-19T01:19:17.000Z","updated_at":"2025-05-01T20:57:59.000Z","dependencies_parsed_at":"2024-08-13T20:09:58.753Z","dependency_job_id":"9d79d344-c347-486b-83a3-f766527821ad","html_url":"https://github.com/nextstrain/mpox","commit_stats":null,"previous_names":["nextstrain/mpox","nextstrain/monkeypox"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fmpox","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fmpox/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fmpox/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fmpox/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextstrain","download_url":"https://codeload.github.com/nextstrain/mpox/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253166520,"owners_count":21864482,"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":["augur","auspice","bioinformatics","genbank","genomic-epidemiology","metadata","monkeypox","mpox","nextstrain","pathogen","phylogenetics","pipeline","virus-evolution"],"created_at":"2024-12-18T23:16:04.515Z","updated_at":"2025-05-09T00:07:26.397Z","avatar_url":"https://github.com/nextstrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Nextstrain repository for mpox virus\n\n[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/nextstrain/mpox/master.svg)](https://results.pre-commit.ci/latest/github/nextstrain/mpox/master)\n\nThis repository contains three workflows for the analysis of mpox virus (MPXV) data:\n\n- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3\n- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization\n- [`nextclade/`](./nextclade) - Make Nextclade datasets for nextstrain/nextclade_data\n\nEach folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/mpox](https://nextstrain.org/mpox).\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## Quickstart\n\nRun the default phylogenetic workflow via:\n```\ncd phylogenetic/\nnextstrain build .\nnextstrain view .\n```\n\n## Documentation\n\n- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)\n- [Contributor documentation](./CONTRIBUTING.md)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fmpox","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextstrain%2Fmpox","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fmpox/lists"}