Metadata-Version: 2.4
Name: ganon
Version: 2.1.1
Summary: ganon classifies DNA sequences against large sets of genomic reference sequences efficiently
Home-page: https://www.github.com/pirovc/ganon
Author: Vitor C. Piro
License: MIT
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
License-File: LICENSE
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: summary

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

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[ganon2 pre-print](https://www.biorxiv.org/content/10.1101/2023.12.07.570547)

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/
