How-to guides

Each guide here solves a single goal and assumes you already have the basics from Getting started.

• Classify a directory of bins: the recommended workflow, one bin per FASTA file.
• Run on an HPC cluster: run with the Apptainer wrapper, no local install needed.
• Classify contigs separately: treat each contig of a metagenome as its own genome.
• Build a species tree: a genome-level supermatrix tree and nearest-reference placement.
• Tune speed and accuracy: fast mode, tree method, and thread layout.
• Configure the database: set the database location, share it, and keep it current.
• Assess genome quality: decide whether a GVMAG is high quality.

Tip

For exact flag definitions see the CLI reference and the output columns. For the reasoning behind each step, follow into Explanation.