{"id":20504172,"url":"https://github.com/haradama/phash","last_synced_at":"2025-03-05T20:46:04.762Z","repository":{"id":152488015,"uuid":"160597327","full_name":"haradama/pHash","owner":"haradama","description":"Software to identify known plasmid sequence from metagenomic assembly using Minhash","archived":false,"fork":false,"pushed_at":"2019-01-29T06:32:53.000Z","size":16688,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-16T07:37:57.584Z","etag":null,"topics":["bioinformatics","biology","contigs","fasta","golang","metagenome","metagenomics","minhash","plasmid","plasmids"],"latest_commit_sha":null,"homepage":"","language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-12-06T00:45:23.000Z","updated_at":"2022-02-25T13:43:56.000Z","dependencies_parsed_at":"2023-06-03T13:30:30.189Z","dependency_job_id":null,"html_url":"https://github.com/haradama/pHash","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FpHash","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FpHash/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FpHash/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haradama%2FpHash/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haradama","download_url":"https://codeload.github.com/haradama/pHash/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242100932,"owners_count":20071823,"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","biology","contigs","fasta","golang","metagenome","metagenomics","minhash","plasmid","plasmids"],"created_at":"2024-11-15T19:36:43.160Z","updated_at":"2025-03-05T20:46:04.730Z","avatar_url":"https://github.com/haradama.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"./pHash_logo.svg\" width=\"40%\" alt=\"pHash\"\u003e\n\npHash is a software to identify known plasmid from metagenomic assembly with the very lightweight database.\n\n## Installation\npHash is available in release page:(https://github.com/haradama/pHash/releases)\n\n## Usage\n\nPlease download the plasmid database file on Zenodo: (http://doi.org/10.5281/zenodo.1991549)\n\n```\nIdentifier of plasmid using database\n\nUsage:\n  pHash identify [flags]\n\nFlags:\n  -d, --db string       Database\n  -h, --help            help for identify\n  -i, --in string       Input FASTA file\n  -k, --kmer int        Length of k-mer (default 17)\n  -o, --out string      Output FASTA file\n  -p, --paralell int    Number of parallel processing (default 4)\n  -s, --sketch int      Sketch size (default 1024)\n  -t, --threshold int   Threshold of probability (default 10)\n```\n\nfor example,\n```\npHash identify -d PLASMID_DATABASE -i YOUR_METAGEMOMIC_DATA\n```\nIf you want to build your own database, please execute the following command.\n```\npHash makedb -i YOUR_PLASMID_DATA -o YOUR_DATABASE_NAME\n```\n\n## Test\n```\nsh ./tests/install_test_data.sh\npHash identify -d plasmidDB11062018.phash -i testData.fna\n```\n\n## License\n\n[GNU General Public License v3.0](https://github.com/haradama/pHash/blob/master/LICENSE)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fharadama%2Fphash","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fharadama%2Fphash","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fharadama%2Fphash/lists"}