ganon 
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 24For further examples, database build guides, installation from source and more: https://pirovc.github.io/ganon/