1. Quick Start

Command Structure

btyper3 -i [fasta] -o [output directory] [options...]

For help, type btyper3 -h or btyper3 --help

For your current version, type btyper3 --version

Sample Commands

Perform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory

Perform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (fastANI is not in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --fastani_path /path/to/FastANI_executable/fastANI

Perform all default analyses, plus pseudo-gene flow unit assignment AND species type strain comparison, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --ani_geneflow True --ani_typestrains True

Perform seven-gene MLST only, using user-supplied MLST gene sequences and the latest version of the PubMLST B. cereus s.l. database (sequences can be in multi-FASTA format, or concatenated into a single sequence in FASTA format):

btyper3 -i /path/to/mlst.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --panC False --download_mlst_latest True

Perform panC group assignment only, using a user-supplied panC gene sequence in FASTA format:

btyper3 -i /path/to/panC.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --mlst False

Perform virulence factor and Bt toxin-encoding gene detection in a plasmid sequence in FASTA format:

btyper3 -i /path/to/plasmid.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --mlst False --panC False