{"id":19885192,"url":"https://github.com/srom/assembly","last_synced_at":"2026-05-15T14:03:25.113Z","repository":{"id":260315280,"uuid":"861671341","full_name":"srom/assembly","owner":"srom","description":"Fetch and process genome assembly data from NCBI.","archived":false,"fork":false,"pushed_at":"2024-11-29T14:49:09.000Z","size":25219,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-11-28T02:19:29.523Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/srom.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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}},"created_at":"2024-09-23T10:16:50.000Z","updated_at":"2024-11-29T14:49:12.000Z","dependencies_parsed_at":"2025-01-11T18:42:11.094Z","dependency_job_id":"4ba256dd-814b-4ace-995d-1cbfb7b185a1","html_url":"https://github.com/srom/assembly","commit_stats":null,"previous_names":["srom/assembly"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/srom/assembly","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Fassembly","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Fassembly/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Fassembly/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Fassembly/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/srom","download_url":"https://codeload.github.com/srom/assembly/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Fassembly/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33068894,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-15T11:35:32.926Z","status":"ssl_error","status_checked_at":"2026-05-15T11:35:31.362Z","response_time":103,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2024-11-12T17:33:32.093Z","updated_at":"2026-05-15T14:03:25.079Z","avatar_url":"https://github.com/srom.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Assembly\n----------\n\nFetch and process genome assembly data from [NCBI](https://www.ncbi.nlm.nih.gov/).\n\n\n## Installation\n\n### Locally with conda\n\n```sh\ngit clone https://github.com/srom/assembly.git\ncd assembly\nconda env create -f environment.yml\nconda activate assembly\n```\n\n### Pip\n\nPyPI package TBD.\n\n### Conda\n\nConda package TBD.\n\n## Run\n\n### Download genomes from NCBI\n\nPrepare text file with one assembly accession per file, e.g.:\n\n```\nGCA_018222585.1\nGCF_000337575.1\nGCA_016840645.1\nGCA_dummy0001.1\n```\n\nNon-existent accessions (such as the last one above) are logged and reported in a file (`missing-accessions.txt`), but they won't make the execution fail and other genomes will still get downloaded. \n\nRun command:\n\n```sh\npython -m src.fetch_assemblies -l test_data/assembly_accessions.txt -o test_data\n```\n\n### Predict coding sequences (CDS) with Prodigal (optional)\n\nAutomatically only runs on genomes without protein fasta file available. Suitable for prokaryotes or phages. [Prodigal](https://github.com/hyattpd/Prodigal) must be installed.\n\n```sh\npython -m src.postprocessing.predict_cds -i test_data\n```\n\n### Concatenate all proteins sequences in one fasta file (optional)\n\n```sh\npython -m src.postprocessing.concatenate_proteins -i test_data -o test_data/all_proteins.fasta\n```\n\n## Outputs\n\nSee example output in folder [`test_data/`](test_data), generated with [`run_test.sh`](run_test.sh).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsrom%2Fassembly","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsrom%2Fassembly","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsrom%2Fassembly/lists"}