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ganon GitHub release (latest by date)

Build Status codecov Anaconda-Server Badge Anaconda-Server Badge install with bioconda Publication

ganon2 pre-print

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

# 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/