{"id":27303020,"url":"https://github.com/tseemann/polyfix","last_synced_at":"2025-08-22T12:35:03.872Z","repository":{"id":146772967,"uuid":"141533785","full_name":"tseemann/polyfix","owner":"tseemann","description":"🔪⛓️ Repair nanopore assemblies using related genome(s)","archived":false,"fork":false,"pushed_at":"2019-08-19T08:05:20.000Z","size":21,"stargazers_count":5,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-28T17:07:09.163Z","etag":null,"topics":["correction","genome-assembly","indel-finder","nanopore-sequencing","reference-genome"],"latest_commit_sha":null,"homepage":"","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-07-19T06:25:02.000Z","updated_at":"2020-11-28T20:02:43.000Z","dependencies_parsed_at":null,"dependency_job_id":"574b3c0e-60f5-4b77-9b98-d9d38391e639","html_url":"https://github.com/tseemann/polyfix","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/tseemann/polyfix","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fpolyfix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fpolyfix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fpolyfix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fpolyfix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tseemann","download_url":"https://codeload.github.com/tseemann/polyfix/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tseemann%2Fpolyfix/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271638720,"owners_count":24794749,"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","status":"online","status_checked_at":"2025-08-22T02:00:08.480Z","response_time":65,"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":["correction","genome-assembly","indel-finder","nanopore-sequencing","reference-genome"],"created_at":"2025-04-12T02:49:41.090Z","updated_at":"2025-08-22T12:35:03.864Z","avatar_url":"https://github.com/tseemann.png","language":"Perl","readme":"[![Build Status](https://travis-ci.org/tseemann/polyfix.svg?branch=master)](https://travis-ci.org/tseemann/polyfix)\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# polyfix\n\n## Introduction\n\nGenomes assembled from Nanopore data are imperfect.  Even at 99.9% consensus\naccuracy there remains ~1 error per 1000 bp.  Given a typical bacterial gene\nis ~1000 bp, this means 1 error per gene.  The most common error mode in\nNanopore is indels, usually around homopolymer regions.  This results in a\nframe-shift in the gene, causing annotation tools like Prokka to find two\npartial genes instead of one intact gene.\n\nIdeally one would also sequence with Illumina and polish the assembly, as\nIllumina data does not suffer from homopolymer issues.  However, if you are\nunable to do that, `polyfix` is designed to take your draft Nanopore\nassembly and compare it to one or more \"trusted reference\" genomes, and\npolish out likely homopolymer errors to remove the frame-shifts. \n\n## Quick Start\n\n```\n% polyfix --version\npolyfix 0.0.1\n\n% polyfix --help\n\n```\n\n## Installation\n\n### Conda\nInstall [Conda](https://conda.io/docs/) or [Miniconda](https://conda.io/miniconda.html):\n```\nconda install -c conda-forge -c bioconda -c defaults polyfix  # COMING SOON\n```\n\n### Homebrew\nInstall [HomeBrew](http://brew.sh/) (Mac OS X) or [LinuxBrew](http://linuxbrew.sh/) (Linux).\n```\nbrew install brewsci/bio/polyfix  # COMING SOON\n```\n\n### Source\nThis will install the latest version direct from Github.\nYou'll need to add the polyfix `bin` directory to your `$PATH`,\nand also ensure all the [dependencies](#Dependencies) are installed.\n```\ncd $HOME\ngit clone https://github.com/tseemann/polyfix.git\n$HOME/polyfix/bin/polyfix --help\n```\n\n## Dependencies\n\n* `perl` \u003e= 5.26\n\n## License\n\npolyfix is free software, released under the\n[GPL 3.0](https://raw.githubusercontent.com/tseemann/polyfix/master/LICENSE).\n\n## Issues\n\nPlease submit suggestions and bug reports to the\n[Issue Tracker](https://github.com/tseemann/polyfix/issues)\n\n## Author\n\n[Torsten Seemann](https://twitter.com/torstenseemann)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fpolyfix","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftseemann%2Fpolyfix","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fpolyfix/lists"}