{"id":45991823,"url":"https://github.com/pirovc/ganon","last_synced_at":"2026-02-28T20:51:18.067Z","repository":{"id":37733859,"uuid":"146760061","full_name":"pirovc/ganon","owner":"pirovc","description":"ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more","archived":false,"fork":false,"pushed_at":"2026-02-05T18:49:26.000Z","size":27958,"stargazers_count":103,"open_issues_count":1,"forks_count":13,"subscribers_count":4,"default_branch":"master","last_synced_at":"2026-02-06T02:30:06.973Z","etag":null,"topics":["bioinformatics","bloom-filter","genbank","gtdb","k-mer","metagenomics","microbiome","minimizers","ncbi","refseq","taxonomy"],"latest_commit_sha":null,"homepage":"https://pirovc.github.io/ganon/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pirovc.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2018-08-30T14:15:57.000Z","updated_at":"2026-02-05T18:36:05.000Z","dependencies_parsed_at":"2026-01-06T05:06:46.015Z","dependency_job_id":null,"html_url":"https://github.com/pirovc/ganon","commit_stats":null,"previous_names":[],"tags_count":35,"template":false,"template_full_name":null,"purl":"pkg:github/pirovc/ganon","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pirovc%2Fganon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pirovc%2Fganon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pirovc%2Fganon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pirovc%2Fganon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pirovc","download_url":"https://codeload.github.com/pirovc/ganon/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pirovc%2Fganon/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29951659,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-28T18:42:55.706Z","status":"ssl_error","status_checked_at":"2026-02-28T18:42:48.811Z","response_time":90,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["bioinformatics","bloom-filter","genbank","gtdb","k-mer","metagenomics","microbiome","minimizers","ncbi","refseq","taxonomy"],"created_at":"2026-02-28T20:51:17.414Z","updated_at":"2026-02-28T20:51:18.059Z","avatar_url":"https://github.com/pirovc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ganon [![GitHub release (latest by date)](https://img.shields.io/github/v/release/pirovc/ganon)](https://github.com/pirovc/ganon)\n\n[![Build Status](https://app.travis-ci.com/pirovc/ganon.svg?token=q6Nfx8pLHh8hV3hLz3Pq\u0026branch=master)](https://app.travis-ci.com/pirovc/ganon) [![codecov](https://codecov.io/gh/pirovc/ganon/branch/master/graph/badge.svg)](https://codecov.io/gh/pirovc/ganon) [![Anaconda-Server Badge](https://anaconda.org/bioconda/ganon/badges/downloads.svg)](https://anaconda.org/bioconda/ganon) [![Anaconda-Server Badge](https://anaconda.org/bioconda/ganon/badges/platforms.svg)](https://anaconda.org/bioconda/ganon) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/ganon/README.html) [![Publication](https://img.shields.io/badge/DOI-10.1093/nargab/lqaf094-blue)](https://dx.doi.org/10.1093/nargab/lqaf094)\n\nganon2 classifies DNA sequences against large sets of genomic reference sequences efficiently. It features:\n\n- integrated download and build of any subset from RefSeq/Genbank/GTDB with incremental updates\n- NCBI and GTDB native support for taxonomic classification, custom taxonomy or no taxonomy at all\n- customizable database build for local or non-standard sequence files\n- optimized taxonomic binning and classification configurations\n- build and classify at various taxonomic levels, strain, assembly, file, sequence or custom specialization\n- hierarchical classification using several databases in one or more levels in just one run\n- EM and/or LCA algorithms to solve multiple-matching reads\n- reporting of multiple and unique matches for every read\n- reporting of sequence, taxonomic or multi-match abundances with optional genome size correction\n- advanced tree-like reports with several filter options\n- generation of contingency tables with several filters for multi-sample studies\n\nFind out more information in the user manual: https://pirovc.github.io/ganon/\n\n## Quick install and usage\n\n```sh\n# Install\nconda install -c bioconda -c conda-forge ganon\n# Download and Build (Archaea - complete genomes - NCBI RefSeq)\nganon build --db-prefix arc_cg_rs --source refseq --organism-group archaea --complete-genomes --threads 24\n# Classify\nganon classify --db-prefix arc_cg_rs --output-prefix classify_results --paired-reads my_reads.1.fq.gz my_reads.2.fq.gz --threads 24\n```\n\nFor further examples, database build guides, installation from source and more: https://pirovc.github.io/ganon/","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpirovc%2Fganon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpirovc%2Fganon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpirovc%2Fganon/lists"}