https://github.com/pirovc/ganon

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
https://github.com/pirovc/ganon

bioinformatics bloom-filter genbank gtdb k-mer metagenomics microbiome minimizers ncbi refseq taxonomy

Last synced: 28 days ago
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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

• Host: GitHub
• URL: https://github.com/pirovc/ganon
• Owner: pirovc
• License: mit
• Created: 2018-08-30T14:15:57.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2026-02-05T18:49:26.000Z (about 2 months ago)
• Last Synced: 2026-02-06T02:30:06.973Z (about 2 months ago)
• Topics: bioinformatics, bloom-filter, genbank, gtdb, k-mer, metagenomics, microbiome, minimizers, ncbi, refseq, taxonomy
• Language: Python
• Homepage: https://pirovc.github.io/ganon/
• Size: 26.7 MB
• Stars: 103
• Watchers: 4
• Forks: 13
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# ganon [![GitHub release (latest by date)](https://img.shields.io/github/v/release/pirovc/ganon)](https://github.com/pirovc/ganon)

[![Build Status](https://app.travis-ci.com/pirovc/ganon.svg?token=q6Nfx8pLHh8hV3hLz3Pq&branch=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)

ganon2 classifies DNA sequences against large sets of genomic reference sequences efficiently. It features:

- integrated download and build of any subset from RefSeq/Genbank/GTDB with incremental updates

- NCBI and GTDB native support for taxonomic classification, custom taxonomy or no taxonomy at all

- customizable database build for local or non-standard sequence files

- optimized taxonomic binning and classification configurations

- build and classify at various taxonomic levels, strain, assembly, file, sequence or custom specialization

- hierarchical classification using several databases in one or more levels in just one run

- EM and/or LCA algorithms to solve multiple-matching reads

- reporting of multiple and unique matches for every read

- reporting of sequence, taxonomic or multi-match abundances with optional genome size correction

- advanced tree-like reports with several filter options

- generation of contingency tables with several filters for multi-sample studies

Find out more information in the user manual: https://pirovc.github.io/ganon/

## Quick install and usage

```sh

# Install

conda install -c bioconda -c conda-forge ganon

# Download and Build (Archaea - complete genomes - NCBI RefSeq)

ganon build --db-prefix arc_cg_rs --source refseq --organism-group archaea --complete-genomes --threads 24

# Classify

ganon classify --db-prefix arc_cg_rs --output-prefix classify_results --paired-reads my_reads.1.fq.gz my_reads.2.fq.gz --threads 24

```

For further examples, database build guides, installation from source and more: https://pirovc.github.io/ganon/