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gtdbtk classify_wf --genome_dir <my_genomes> --out_dir <output_dir> (--skip_ani_screen OR --mash_db)
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This will process all genomes in the directory <my_genomes> using both bacterial and archaeal marker sets and place the results in <output_dir>. Genomes must be in FASTA format (gzip with the extension .gz is acceptable).
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The location of genomes can also be specified using a batch file with the ``--batchfile`` flag. The batch file is a two column file indicating the location of each genome and the desired genome identifier
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