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
ganon2 classifies DNA sequences against large sets of genomic reference sequences efficiently. It features:
Find out more information in the user manual: https://pirovc.github.io/ganon/
# 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/