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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":["amplicon","bioconductor","bioinformatics","metabarcoding","metagenomics","microbiome","taxonomy"],"created_at":"2025-10-20T14:35:54.782Z","updated_at":"2026-02-18T20:31:44.567Z","avatar_url":"https://github.com/benjjneb.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n[![Build Status](https://github.com/benjjneb/dada2/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/benjjneb/dada2/actions/workflows/pages/pages-build-deployment)\n\n# dada2\n\nExact sample inference from high-throughput amplicon data. Resolves real variants differing by as little as one nucleotide. Visit [the DADA2 website](https://benjjneb.github.io/dada2/index.html) for the most detailed and up-to-date documentation.\n\n### Installation\n\nThe dada2 package binaries are available through Bioconductor:\n\n```S\n## try http:// if https:// URLs are not supported\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"dada2\")\n```\n\nIn order to install dada2 from source (and get the latest and greatest new features) see our [installation from source instructions](https://benjjneb.github.io/dada2/dada-installation.html).\n\n### Documentation\n\nThe [tutorial walkthrough of the DADA2 pipeline on paired end Illumina Miseq data](https://benjjneb.github.io/dada2/tutorial.html). \n\nThe [dada2 R package manual](https://www.bioconductor.org/packages/3.6/bioc/manuals/dada2/man/dada2.pdf).\n\nFurther documentation is available on [the DADA2 front page](http://benjjneb.github.io/dada2/). \n\n### DADA2 Articles\n\n[DADA2: High resolution sample inference from Illumina amplicon data. Nature Methods, 2016.](http://dx.doi.org/10.1038/nmeth.3869) [(Open Access link.)](http://rdcu.be/ipGh)\n\n[Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000 Research, 2016.](https://f1000research.com/articles/5-1492)\n\n[Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISMEJ, 2017.](http://dx.doi.org/10.1038/ismej.2017.119)\n\n[High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 2019.](http://dx.doi.org/10.1093/nar/gkz569)\n\n### Other Resources\n\nPlanned feature improvements are publicly catalogued at the main DADA2 development site on github, specifically on the \"Issues\" page for DADA2:\n\nhttps://github.com/benjjneb/dada2/issues\n\nIf the feature you are hoping for is not listed, you are welcome to add it as a feature request \"issue\" on this page. This request will be publicly available and listed on the page.\n\nBugs and difficulties in using DADA2 are also welcome on [the issue tracker](https://github.com/benjjneb/dada2/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenjjneb%2Fdada2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenjjneb%2Fdada2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenjjneb%2Fdada2/lists"}