{"id":18448419,"url":"https://github.com/nextomics/nextpolish","last_synced_at":"2025-04-04T11:11:13.630Z","repository":{"id":50468210,"uuid":"185516643","full_name":"Nextomics/NextPolish","owner":"Nextomics","description":" Fast and accurately polish the genome generated by long reads.","archived":false,"fork":false,"pushed_at":"2025-01-09T01:21:21.000Z","size":14898,"stargazers_count":219,"open_issues_count":44,"forks_count":28,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-03-28T10:06:41.012Z","etag":null,"topics":["assembly","genome","polish"],"latest_commit_sha":null,"homepage":"","language":"C","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/Nextomics.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":"2019-05-08T02:54:34.000Z","updated_at":"2025-03-14T22:15:18.000Z","dependencies_parsed_at":"2022-09-13T17:50:28.427Z","dependency_job_id":"c48a48d2-316b-4665-8680-c1cd2d28ed3f","html_url":"https://github.com/Nextomics/NextPolish","commit_stats":{"total_commits":67,"total_committers":1,"mean_commits":67.0,"dds":0.0,"last_synced_commit":"d864a9ba2c42f3be8d67c0164e32754f263e5f08"},"previous_names":[],"tags_count":17,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextPolish","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextPolish/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextPolish/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextPolish/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Nextomics","download_url":"https://codeload.github.com/Nextomics/NextPolish/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247166168,"owners_count":20894654,"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":["assembly","genome","polish"],"created_at":"2024-11-06T07:15:50.469Z","updated_at":"2025-04-04T11:11:13.613Z","avatar_url":"https://github.com/Nextomics.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Release](https://img.shields.io/github/release/Nextomics/NextPolish.svg)](https://github.com/Nextomics/NextPolish/releases)\n[![Documentation Status](https://readthedocs.org/projects/nextpolish/badge/?version=latest)](https://nextpolish.readthedocs.io/en/latest/?badge=latest)\n\n# NextPolish\nNextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct/assemble the raw third-generation sequencing (TGS) long reads with approximately 10-15% sequencing errors, please use [NextDenovo](https://github.com/Nextomics/NextDenovo). To further improve the consensus accuracy of genomes assembled using HiFi long-reads, please use [NextPolish2](https://github.com/Nextomics/NextPolish2).\n\n## Installation\n\n* **DOWNLOAD**  \nclick [here](https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish.tgz) or use the following command:  \n`wget https://github.com/Nextomics/NextPolish/releases/download/v1.4.1/NextPolish.tgz`  \n\n\t***Note:*** If you get an error like `version 'GLIBC_2.14' not found` or `liblzma.so.0: cannot open shared object file`, Please download [this version](https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish-CentOS6.9.tgz).\n\n* **REQUIREMENT**  \n\t* [Python](https://www.python.org/download/releases/) (Support python 2 and 3):\n\t\t* [Paralleltask](https://github.com/moold/ParallelTask)\n\n* **INSTALL**  \n```\npip install paralleltask\ntar -vxzf NextPolish.tgz \u0026\u0026 cd NextPolish \u0026\u0026 make\n```\n\n* **UNINSTALL**  \n`cd NextPolish \u0026\u0026 make clean`\n\n* **TEST**  \n`nextPolish test_data/run.cfg`\n\n## Learn\n\n* [Quick Start](https://nextpolish.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and try now\n* [Tutorial](https://nextpolish.readthedocs.io/en/latest/TUTORIAL.html) - step by step introduction to polish a genome with different types of data\n* [FAQ](https://nextpolish.readthedocs.io/en/latest/FAQ.html) - frequently asked questions\n* [Parameter Reference](https://nextpolish.readthedocs.io/en/latest/OPTION.html) - a detailed introduction about all the parameters\n* [Cite](https://nextpolish.readthedocs.io/en/latest/QSTART.html#cite) - if you get a high accuracy assembly with NextPolish, please cite it\n\n## Star\n\nYou can track updates by tab the `Star` button on the upper-right corner at this page.\n\n## More\n\nThe complete user documentation is available [here](https://nextpolish.readthedocs.io/en/latest/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Fnextpolish","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextomics%2Fnextpolish","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Fnextpolish/lists"}