{"id":22632758,"url":"https://github.com/mtvector/cleanome","last_synced_at":"2026-02-25T02:31:17.877Z","repository":{"id":221066169,"uuid":"753334115","full_name":"mtvector/cleanome","owner":"mtvector","description":"Download genome annotations and prepare them to be made into reference annotations (e.g. with cellranger or cellranger-arc)","archived":false,"fork":false,"pushed_at":"2025-06-24T22:20:47.000Z","size":125,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-24T23:27:29.337Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mtvector.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,"zenodo":null}},"created_at":"2024-02-05T23:01:11.000Z","updated_at":"2025-06-24T22:20:52.000Z","dependencies_parsed_at":"2024-02-11T01:25:43.827Z","dependency_job_id":"45d7ae0d-a1eb-44c8-b9af-e7d84ae1a16a","html_url":"https://github.com/mtvector/cleanome","commit_stats":null,"previous_names":["mtvector/cleanome"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mtvector/cleanome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtvector%2Fcleanome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtvector%2Fcleanome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtvector%2Fcleanome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtvector%2Fcleanome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mtvector","download_url":"https://codeload.github.com/mtvector/cleanome/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtvector%2Fcleanome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29809086,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-24T22:43:48.403Z","status":"online","status_checked_at":"2026-02-25T02:00:07.329Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-12-09T02:20:10.713Z","updated_at":"2026-02-25T02:31:17.847Z","avatar_url":"https://github.com/mtvector.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# cleanome\nThis is a python package that can be used to download genome annotations from multiple species and prepare them to be made into reference annotations (e.g. with cellranger or cellranger-arc). It is meant to standardize the process of debugging gtf files in order to make them compatible as gtfs provided by NCBI and ENSEMBL generally have one of a few problems that make them incompatible with creating genomics reference annotations (missing gene/transcript ids, duplicated genes or transcripts, contigs that are too large etc). The package has three functions: 1. Download fasta, gtf, and assembly metadata files for a list of species (by scientific name or taxid). 2. Generate statistics for the assemblies and debug them. 3. Write shell scripts for making [cellranger-arc] references.\n\n\n### Installation\n\nMake a anaconda environment with python\u003e=3.6\n\n```\nconda install -c conda-forge ncbi-datasets-cli\n\nconda install -c conda-forge -c bioconda ete3 gtfparse numpy pandas polars polars-lts-cpu pyarrow requests biopython tqdm \n```\n\n```\ngit clone git@github.com:mtvector/cleanome.git\ncd cleanome\npip install .\n```\n\n### Usage\n\n\nTo debug a gtf by adding missing gene and transcript fields, replacing missing gene fields with the gene_id, and other common issues in NCBI genome annotations:\n\n```\ndebug_gtf file.gtf file.debug.gtf\n```\n\nSee example_run.sh for an example script utilizing the full pipeline to download genomes, get statistics, debug gtfs and build cellranger-arc references.\n\nCurrent pipeline functions include:\n```\ndownload_genomes --species_list ./species.txt --genome_dir ./genomes/\n```\nDownload genomes from NCBI for all the species on the list. A utility for downloading ENSEMBL genomes for the list is included (have to write your own download_genomes.py for now)\n\n```\nget_genomes_and_stats --genome_dir ./genomes/ -o ./genome_info.csv -c\n```\nCollects the fastas and gtfs from all the genomes in a directory and calculates some simple statistics. \n\n```\nmake_cellranger_arc_sh --sh_scripts_dir ./submission_scripts/ --stats_csv ./genome_info.csv --output_dir ~/cellranger-arc --log_dir ~/log/ -cellranger_bin /path/to/cellranger-arc/bin/\n```\n\nDebugs gtfs (deduplicate transcripts/genes, add missing transcripts for exons and missing genes for transcripts, fills missing values with placeholders, split chromosomes that are too large, fix nesting)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmtvector%2Fcleanome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmtvector%2Fcleanome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmtvector%2Fcleanome/lists"}