ganon2 hands-on - 2026-06-17:)

This tutorial introduces practical approaches to creating and utilising databases for metagenomics classification with Ganon2. It will cover both basic and advanced options, as well as common pitfalls in metagenomics classification. Topics include selecting databases and taxonomies, choosing parameters and thresholds, and interpreting results.

By the end, you should have acquired the knowledge required to create your own databases and implement suitable classification strategies to improve your metagenomics analyses.

The tutorial uses real human skin metagenomics samples and enhances their default classification using metagenome-assembled genomes. Reports and a final table of counts are created, and the results are visualised using taxonomic bars and a heatmap.

Prepare files and tools:)

Download files:)

Download prepared files and unpack in a working directory of choice:

mkdir ganon_handson_20260617
cd ganon_handson_20260617
wget ...
tar xf ...

Install tools:)

• ganon

conda create -c conda-forge -c bioconda -n ganonenv ganon

• GRIMER (for visualization)

conda create -n grimerenv -c conda-forge "python=3.9" "biom-format=2.1.16" "numpy=1.23.5"
conda activate grimerenv
conda install "grimer=1.1.0"
conda deactivate

Useful alias to check tsv files:)

# c: like cat but with aligned tabs for tsv files
alias c="column -s$'\t' -t"

# cless: like less with c function above
cless() {
    if [ -z "$1" ]; then
        c | less -SN
    else
        c "$1" | less -SN
    fi
}

If you find them useful, you can add those commands to your ~/.bashrc to have it available at all times.

Check installed version and files:)

Ganon:

$ conda activate ganonenv
$ ganon --version
version: ganon 2.4.2
$ genome_updater.sh | grep -m 1 "v" | tr -d ' '
v0.8.1
$ python -c "import multitax; print(multitax.__version__)"
1.6.0

GRIMER:

$ conda activate grimerenv
$ grimer --version | grep "grimer"
grimer 1.1.0

Files:

$ ls -1 *
ganon_handson_files_20260617.tar.gz

files:
aux
gcmeta
mgnify
reads
rs_bac_cg_ncbi_t1f_files
rs_bac_gtdb_t1f_files