{"id":27303086,"url":"https://github.com/tseemann/phastaf","last_synced_at":"2026-02-15T05:32:18.332Z","repository":{"id":146772963,"uuid":"187126658","full_name":"tseemann/phastaf","owner":"tseemann","description":"Identify phage regions in bacterial genomes for masking purposes","archived":false,"fork":false,"pushed_at":"2019-09-05T00:54:42.000Z","size":19306,"stargazers_count":30,"open_issues_count":3,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-12T02:52:42.332Z","etag":null,"topics":["bacteria","bioinformatics","genomics","phage"],"latest_commit_sha":null,"homepage":null,"language":"Perl","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/tseemann.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":"2019-05-17T01:37:17.000Z","updated_at":"2024-06-18T08:36:31.000Z","dependencies_parsed_at":null,"dependency_job_id":"1f48761f-9c39-40fe-96c9-155e24308d1f","html_url":"https://github.com/tseemann/phastaf","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/tseemann/phastaf","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fphastaf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fphastaf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fphastaf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fphastaf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tseemann","download_url":"https://codeload.github.com/tseemann/phastaf/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fphastaf/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29470614,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-15T05:26:30.465Z","status":"ssl_error","status_checked_at":"2026-02-15T05:26:21.858Z","response_time":118,"last_error":"SSL_read: 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":["bacteria","bioinformatics","genomics","phage"],"created_at":"2025-04-12T02:49:57.721Z","updated_at":"2026-02-15T05:32:18.317Z","avatar_url":"https://github.com/tseemann.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/tseemann/phastaf.svg?branch=master)](https://travis-ci.org/tseemann/phastaf)\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n![Don't judge me](https://img.shields.io/badge/Language-Perl_5-steelblue.svg)\n\n:warning: **THIS SOFTWARE IS STILL IN VERY EARLY DEVELOPMENT!**\n\n# phastaf\n\nIdentify phage regions in bacterial genomes for masking purposes\n\n## Introduction\n\n## Quick Start\n\n```bash\n% head -n 4 contigs.fna\n\u003eAE004092.2 Streptococcus pyogenes M1 GAS, complete genome\nTTGTTGATATTCTGTTTTTTCTTTTTTAGTTTTCCACATGAAAAATAGTTGAAAACAATAGCGGTGTCCC\nCTTAAAATGGCTTTTCCACAGGTTGTGGAGAACCCAAATTAACAGTGTTAATTTATTTTCCACAGGTTGT\nGGAAAAACTAACTATTATCCATCGTTCTGTGGAAAACTAGAATAGTTTATGGTAGAATAGTTCTAGAATT\n\n% phastaf --outdir out contigs.fna\n\n% cat out/phage.bed\nAE004092.2\t529586\t570503\t370.1\nAE004092.2\t778519\t821003\t370.2\nAE004092.2\t1189119\t1222648\t370.3\nAE004092.2\t1773338\t1786887\t370.4\n```\n\n## Installation\n\n### Homebrew\n\n```\nbrew install brewsci/bio/phastaf  # COMING SOON\nphastaf --check\n```\nUsing Homebrew will install all the dependencies for you: \n[Linux](http://linuxbrew.sh) or [MacOS](http://brew.sh)\n\n### Conda\n\n```\nconda install -c bioconda phastaf  # COMING SOON\nphastaf --check\n```\nLearn more about [Bioconda](https://bioconda.github.io/).\n\n### Source\n\n```\ngit clone https://github.com/tseemann/phastaf.git\n./phastaf/bin/phastaf --help\n./phastaf/bin/phastaf --check\n```\nYou will need to install all the dependencies manually:\n* diamond \u003e= 0.9\n* bedtools \u003e= 2.0\n* any2fasta \u003e= 0.4\n* sort (GNU or BSD)\n\n## Feedback\n\nPlease file questions, bugs or ideas \nto the [Issue Tracker](https://github.com/tseemann/phastaf/issues)\n\n## License\n\n[GPLv3](https://raw.githubusercontent.com/tseemann/phastaf/master/LICENSE)\n\n## Citation\n\nNot published yet.\n\n## Authors\n\n* Torsten Seemann\n* Jake Lacey\n* Sharif Shaaban\n* Federica Palma \n* Rebecca Ji Bengtsson\n* Nabil-Fareed Alikhan\n* Carlus Deneke\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fphastaf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftseemann%2Fphastaf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fphastaf/lists"}