{"id":17119728,"url":"https://github.com/lczech/grenedalf","last_synced_at":"2025-07-04T22:32:58.408Z","repository":{"id":47120719,"uuid":"314035818","full_name":"lczech/grenedalf","owner":"lczech","description":"Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence 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install](https://img.shields.io/conda/vn/bioconda/grenedalf)](https://anaconda.org/bioconda/grenedalf)\n[![Downloads](https://img.shields.io/conda/dn/bioconda/grenedalf)](https://anaconda.org/bioconda/grenedalf)\n[![Release](https://img.shields.io/github/v/release/lczech/grenedalf.svg)](https://github.com/lczech/grenedalf/releases)\n![Language](https://img.shields.io/badge/language-C%2B%2B11-lightgrey.svg)\n[![Softwipe Score](https://img.shields.io/badge/softwipe-9.0/10.0-blue)](https://github.com/adrianzap/softwipe/wiki/Code-Quality-Benchmark)\n[![CI](https://github.com/lczech/grenedalf/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/lczech/grenedalf/actions/workflows/ci.yaml)\n[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](http://www.gnu.org/licenses/gpl.html)\n[![DOI](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtaa070-blue)](https://doi.org/10.1093/bioinformatics/btae508)\n\u003c!-- [![CI](https://github.com/lczech/grenedalf/workflows/CI/badge.svg?branch=master)](https://github.com/lczech/grenedalf/actions) --\u003e\n\u003c!-- [![Platforms](https://img.shields.io/conda/pn/bioconda/grenedalf)](https://anaconda.org/bioconda/grenedalf) --\u003e\n\u003c!-- [![Build Status](https://travis-ci.org/lczech/grenedalf.svg?branch=master)](https://travis-ci.org/lczech/grenedalf) --\u003e\n\n![grenedalf](/doc/logo/grenedalf.png?raw=true \"grenedalf\")\n\n\nFeatures\n-------------------\n\ngrenedalf is a collection of commands for working with pool sequencing population genetic data.\nIts main focus are statistical analyses such as Tajima's D and Fst, as well as convenience functions around pool sequencing data.\nThe statistics follow the approaches of [PoPoolation](https://sourceforge.net/projects/popoolation/)\nand [PoPoolation2](https://sourceforge.net/projects/popoolation2/),\nas well as [poolfstat](https://cran.r-project.org/web/packages/poolfstat/index.html)\nand [npstat](https://github.com/lucaferretti/npstat). However, compared to those, grenedalf\nis significantly more scalable, more user friendly, and offers more settings and input file formats.\n\n\nSetup\n-------------------\n\nWe recommend to first try the pre-compiled binaries of the latest [Release](https://github.com/lczech/grenedalf/releases), by downloading the binary for your system from the \"Assets\" list below the release. Alternatively, grenedalf can be installed via [bioconda](https://anaconda.org/bioconda/grenedalf). If that does not work, it can be build from source as described [here](https://github.com/lczech/grenedalf/wiki/Setup). If you want the best performance, we recommend to build from source anyway.\n\n\nUsage and Documentation\n-------------------\n\ngrenedalf is used via its command line interface, with commands for each task.\nThe commands have the general structure:\n\u003c!-- grenedalf \u003cmodule\u003e \u003csubcommand\u003e \u003coptions\u003e --\u003e\n\n    grenedalf \u003ccommand\u003e \u003coptions\u003e\n\nSee [**the Wiki pages**](https://github.com/lczech/grenedalf/wiki) for the list of all commands and their documentation.\n\n\u003c!-- # grenedalf\nGenome Analyses of Differential Allele Frequencies --\u003e\n\n\nSupport and Requests\n-------------------\n\nFor **questions, bug reports, and feature requests**, please [open an issue](https://github.com/lczech/grenedalf/issues). Please do not send emails with questions or requests, as others might be having them as well, and so it is better to discuss them here where they can be found.\n\nFeedback on functionality, interface, and features is highly appreciated, as we are always open to discussing new statistics and tools that might be relevant for the community. If you need other pool sequencing statistics than the ones already offered here, please reach out - happy to explore the potential for a collaboration there! We have a lot of code infrastructure in grenedalf that takes care of all the basics, and so it would be nice to implement further statistics!\n\n\nCitation\n-------------------\n\nPlease find the publication here:\n\n\u003e grenedalf: population genetic statistics for the next generation of pool sequencing.\u003cbr /\u003e\n\u003e Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.\u003cbr /\u003e\n\u003e Bioinformatics, 2024. doi:[10.1093/bioinformatics/btae508](https://doi.org/10.1093/bioinformatics/btae508)\n\nEach command also prints out the relevant references for that command. Then, the command [`grenedalf citation`](https://github.com/lczech/grenedalf/wiki/Subcommand:-citation) can be used to obtain details on those references.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgrenedalf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flczech%2Fgrenedalf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flczech%2Fgrenedalf/lists"}