It uses GTDB-tk to taxonomically annotate your genomes and to build a tree.
Run as follows:
dbdir="databases"
genome_dir="genomes"
snakemake --use-conda --conda-prefix "$dbdir/conda_envs" \
--config database_dir="$dbdir" genome_dir="$genome_dir"
where dbdir is the path to a (shared) directory to place the GTDB database and conda envs.
genome_dir should be the folder containing all genome fastas.
This code was developped as part of metagenome-atlas. Don't forget to cite the GTDB-tk