{"id":43316336,"url":"https://github.com/will-rowe/groot","last_synced_at":"2026-02-01T22:03:45.649Z","repository":{"id":144210063,"uuid":"117543539","full_name":"will-rowe/groot","owner":"will-rowe","description":"A resistome profiler for Graphing Resistance Out Of 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returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while 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":["alignment","antibiotic-resistance","lsh","metagenomics","minhash","resistome"],"created_at":"2026-02-01T22:03:45.167Z","updated_at":"2026-02-01T22:03:45.638Z","avatar_url":"https://github.com/will-rowe.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv align=\"center\"\u003e\n    \u003cimg src=\"misc/groot-logo-with-text.png?raw=true?\" alt=\"groot-logo\" width=\"250\"\u003e\n    \u003ch3\u003e\u003ca style=\"color:#D5672C\"\u003eG\u003c/a\u003eraphing \u003ca style=\"color:#D5672C\"\u003eR\u003c/a\u003eesistance \u003ca style=\"color:#D5672C\"\u003eO\u003c/a\u003eut \u003ca style=\"color:#D5672C\"\u003eO\u003c/a\u003ef me\u003ca style=\"color:#D5672C\"\u003eT\u003c/a\u003eagenomes\u003c/h3\u003e\n    \u003chr\u003e\n    \u003ca href=\"https://travis-ci.org/will-rowe/groot\"\u003e\u003cimg src=\"https://travis-ci.org/will-rowe/groot.svg?branch=master\" alt=\"travis\"\u003e\u003c/a\u003e\n    \u003ca href='http://groot-documentation.readthedocs.io/en/latest/?badge=latest'\u003e\u003cimg src='https://readthedocs.org/projects/groot-documentation/badge/?version=latest' alt='Documentation Status' /\u003e\u003c/a\u003e\n    \u003ca href=\"https://goreportcard.com/report/github.com/will-rowe/groot\"\u003e\u003cimg src=\"https://goreportcard.com/badge/github.com/will-rowe/groot\" alt=\"reportcard\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/will-rowe/groot/blob/master/LICENSE\"\u003e\u003cimg src=\"https://img.shields.io/badge/license-MIT-orange.svg\" alt=\"License\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://zenodo.org/badge/latestdoi/117543539\"\u003e\u003cimg src=\"https://zenodo.org/badge/117543539.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://gitter.im/groot-help/Lobby\"\u003e\u003cimg src=\"https://img.shields.io/badge/chat-gitter-8A2BE2.svg\" alt=\"bioconda\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://bioconda.github.io/recipes/groot/README.html\"\u003e\u003cimg src=\"https://anaconda.org/bioconda/groot/badges/downloads.svg\" alt=\"bioconda\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://media.giphy.com/media/3o7budMRwZvNGJ3pyE/giphy.gif\"\u003e\u003cimg src=\"https://img.shields.io/badge/i%20am-groot-green.svg\" alt=\"bioconda\"\u003e\u003c/a\u003e\n\u003c/div\u003e\n\n---\n\n## Overview\n\n`GROOT` is a tool to type **Antibiotic Resistance Genes** (**ARGs**) in metagenomic samples (a.k.a. **Resistome Profiling**). It combines variation graph representation of gene sets with an LSH indexing scheme to allow for fast classification of metagenomic reads. Subsequent hierarchical local alignment of classified reads against graph traversals facilitates accurate reconstruction of full-length gene sequences using a simple scoring scheme.\n\n`GROOT` will output an ARG alignment file (in BAM format) that contains the graph traversals possible for each query read; the alignment file is then used by `GROOT` to generate a resistome profile.\n\nSince version 0.4, `GROOT` will also output the variation graphs which had reads align. These graphs are in [GFA format](https://github.com/GFA-spec/GFA-spec), allowing you to visualise graph alignments using [Bandage](https://github.com/rrwick/Bandage) and determine which variants of a given ARG type are dominant in your metagenomes. Read the [documentation](http://groot-documentation.readthedocs.io/en/latest/?badge=latest) for more info.\n\nSince version 1.0.0, `GROOT` has had a partial re-write (merging features and changes from my [baby groot](https://github.com/will-rowe/baby-groot) project). It now uses the excellent [LSH Ensemble library](https://github.com/ekzhu/lshensemble) as the LSH index, enabling containment search for read seeding. I've also improved my dev know-how and `GROOT` is now more efficient. However, these changes have meant that I've needed to change some of the CLI, so please read the docs.\n\n## Installation\n\nCheck out the [releases](https://github.com/will-rowe/groot/releases) to download a binary. Alternatively, install using Bioconda or compile the software from source.\n\n### Bioconda\n\n```\nconda install -c bioconda groot\n```\n\n### Brew\n\n```\nbrew install brewsci/bio/groot\n```\n\n### Source\n\n`GROOT` is written in Go (v1.14) - to compile from source you will first need the [Go tool chain](https://golang.org/doc/install). Once you have it, try something like this to compile:\n\n```bash\n# Clone this repository\ngit clone https://github.com/will-rowe/groot.git\n\n# Go into the repository and get the package dependencies\ncd groot\ngo get -d -t -v ./...\n\n# Run the unit tests\ngo test -v ./...\n\n# Compile the program\ngo build ./\n\n# Call the program\n./groot --help\n```\n\n## Quick Start\n\n`GROOT` is called by typing **groot**, followed by the subcommand you wish to run. There are three main subcommands: **index**, **align** and **report**. This quick start will show you how to get things running but it is recommended to follow the [documentation](http://groot-documentation.readthedocs.io/en/latest/?badge=latest).\n\n```bash\n# Get a pre-clustered ARG database\ngroot get -d arg-annot\n\n# Create graphs and index\ngroot index -m arg-annot.90 -i grootIndex -w 100\n\n# Align reads and report\ngroot align -i grootIndex -f reads.fq | groot report\n```\n\n\u003e note: it's recommended to index the graph using a window size ~= your maximum expected read length, so for 100bp reads, use `-w 100`\n\n## Further Information \u0026 Citing\n\nPlease [readthedocs](http://groot-documentation.readthedocs.io/en/latest/?badge=latest) for more extensive documentation and a [tutorial](https://groot-documentation.readthedocs.io/en/latest/tutorial.html).\n\n`GROOT` has now been published in Bioinformatics:\n\n\u003e [Rowe WPM, Winn MD. Indexed variation graphs for efficient and accurate resistome profiling. Bioinformatics. 2018. doi: bty387](https://doi.org/10.1093/bioinformatics/bty387)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwill-rowe%2Fgroot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwill-rowe%2Fgroot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwill-rowe%2Fgroot/lists"}