{"id":20504185,"url":"https://github.com/haradama/plasmidpicker","last_synced_at":"2025-04-13T20:48:32.904Z","repository":{"id":152488023,"uuid":"139538625","full_name":"haradama/PlasmidPicker","owner":"haradama","description":"Software to identify plasmid sequence data from metagenome using logistic regression and Minhash","archived":false,"fork":false,"pushed_at":"2018-11-19T10:38:40.000Z","size":139839,"stargazers_count":6,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-13T20:48:20.615Z","etag":null,"topics":["bioinformatics","classification","contigs","fasta","logistic-regression","metagenome","metagenomics","minhash","plasmids"],"latest_commit_sha":null,"homepage":"","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/haradama.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}},"created_at":"2018-07-03T06:31:25.000Z","updated_at":"2020-08-02T03:27:44.000Z","dependencies_parsed_at":null,"dependency_job_id":"821cc3b6-fca8-4ccd-99a8-8f05d2741de0","html_url":"https://github.com/haradama/PlasmidPicker","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/haradama%2FPlasmidPicker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FPlasmidPicker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FPlasmidPicker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FPlasmidPicker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haradama","download_url":"https://codeload.github.com/haradama/PlasmidPicker/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248782280,"owners_count":21160716,"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":["bioinformatics","classification","contigs","fasta","logistic-regression","metagenome","metagenomics","minhash","plasmids"],"created_at":"2024-11-15T19:36:45.002Z","updated_at":"2025-04-13T20:48:32.882Z","avatar_url":"https://github.com/haradama.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![PlasmidPicker](./logo.png)\n\n## Requirements\n- numpy\n- cython\n- biopython\n- click\n- mmh3\n- h5py\n\n## Installation\n\n```\ngit clone https://github.com/haradama/PlasmidPicker.git\ncd PlasmidPicker\npip install -r requirements.txt\npython setup.py install\n```\n\n## Usage\n\n```\nUsage: plasmidpicker pick [OPTIONS]\n\n  Detect plasmid sequence data in metagenome.\n\nOptions:\n  -i, --infile TEXT        Specify FASTA input file\n  -t, --threshold INTEGER  Threshold of probability (0 \u003c= t \u003c= 100) [70]\n  -l, --length INTEGER     Threshold of contig's length [1000]\n  -d, --outdir TEXT        Output directory [.]\n  --help                   Show this message and exit.\n```\n\n```\nUsage: plasmidpicker classify [OPTIONS]\n\n  Perform similarity search of plasmids using MinHash.\n\nOptions:\n  -i, --infile TEXT     Specify FASTA input file\n  -s, --sketch INTEGER  Sketch size (1 \u003c= s \u003c=1000) [1000]\n  -l, --length INTEGER  Threshold of contig's length [1000]\n  -hi, --hits INTEGER   Number of hits to display [5]\n  -o, --outfile TEXT    Output file [result.txt]\n  --help                Show this message and exit.\n```\n\n## License\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fharadama%2Fplasmidpicker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fharadama%2Fplasmidpicker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fharadama%2Fplasmidpicker/lists"}