{"id":15060273,"url":"https://github.com/nextomics/nextdenovo","last_synced_at":"2025-10-07T01:11:09.725Z","repository":{"id":49833484,"uuid":"164813400","full_name":"Nextomics/NextDenovo","owner":"Nextomics","description":"Fast and accurate de novo assembler for long reads","archived":false,"fork":false,"pushed_at":"2024-05-10T01:23:12.000Z","size":14376,"stargazers_count":387,"open_issues_count":48,"forks_count":53,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-04-05T22:07:58.371Z","etag":null,"topics":["assembler","genome-assembly","long-reads","oxford-nanopore","pacbio"],"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":"2019-01-09T07:39:29.000Z","updated_at":"2025-04-03T08:59:47.000Z","dependencies_parsed_at":"2022-07-30T22:07:59.706Z","dependency_job_id":"e479651e-5b18-4dd3-bde7-72252279e161","html_url":"https://github.com/Nextomics/NextDenovo","commit_stats":null,"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextDenovo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextDenovo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextDenovo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FNextDenovo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Nextomics","download_url":"https://codeload.github.com/Nextomics/NextDenovo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247406090,"owners_count":20933803,"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":["assembler","genome-assembly","long-reads","oxford-nanopore","pacbio"],"created_at":"2024-09-24T22:55:31.940Z","updated_at":"2025-10-07T01:11:04.691Z","avatar_url":"https://github.com/Nextomics.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Downloads](https://img.shields.io/github/downloads/Nextomics/NextDenovo/total?logo=github)](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz)\n[![Release](https://img.shields.io/github/release/Nextomics/NextDenovo.svg)](https://github.com/Nextomics/NextDenovo/releases)\n[![Documentation Status](https://readthedocs.org/projects/nextdenovo/badge/?version=latest)](https://nextdenovo.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03252--4-blue)](https://doi.org/10.1186/s13059-024-03252-4)\n\n# NextDenovo\nNextDenovo is a string graph-based *de novo* assembler for long reads (CLR, ~~HiFi~~ and ONT). It uses a \"correct-then-assemble\" strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try [NextPolish](https://github.com/Nextomics/NextPolish).\n\nWe benchmarked NextDenovo against other assemblers using Oxford Nanopore long reads from [human](https://nextdenovo.readthedocs.io/en/latest/TEST2.html) and [Drosophila melanogaster](https://nextdenovo.readthedocs.io/en/latest/TEST4.html), and PacBio continuous long reads (CLR) from [Arabidopsis thaliana](https://nextdenovo.readthedocs.io/en/latest/TEST3.html). NextDenovo produces more contiguous assemblies with fewer contigs compared to the other tools. NextDenovo also shows a high assembly accurate level in terms of assembly consistency and single-base accuracy.\n\n## Installation\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) `pip install paralleltask`\n\n* **INSTALL**  \n\n\tclick [here](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz) or use the following command:   \n\t```sh\n\twget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz\n\ttar -vxzf NextDenovo.tgz \u0026\u0026 cd NextDenovo\n\t```   \n\n\tIf you want to compile from the source, run:\n\n\t```sh\n\tgit clone git@github.com:Nextomics/NextDenovo.git\n\tcd NextDenovo \u0026\u0026 make\n\t```\n\n* **TEST**  \n`nextDenovo test_data/run.cfg`\n\n## Learn\n\n* [Quick Start](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and assemble now\n* [Tutorial](https://nextdenovo.readthedocs.io/en/latest/TEST1.html) - step by step introduction to assemble the HG002 genome\n* [FAQ](https://nextdenovo.readthedocs.io/en/latest/FAQ.html) - frequently asked questions\n* [Parameter Reference](https://nextdenovo.readthedocs.io/en/latest/OPTION.html) - a detailed introduction about all the parameters\n* [Cite](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite) - if you get a good assembly with NextDenovo, 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://nextdenovo.readthedocs.io/en/latest/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Fnextdenovo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextomics%2Fnextdenovo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Fnextdenovo/lists"}