3. Usage and Options

Input File Formats

BTyper3 requires an assembled genome in FASTA format, with one FASTA file containing a single B. cereus group genome (this can be a closed genome, or a draft genome containing multiple contigs or scaffolds)

Users with MLST, panC, and/or plasmid sequences can additionally use BTyper3; sequences should be in FASTA format (both concatenated sequences and multi-FASTA format are fine). However, all ANI-based methods should be set to False, as they are only interpretable for whole genomes. For MLST, panC, and plasmid sample commands, see the Quick Start section of the wiki.

Required Arguments

BTyper3 can be run from your terminal with the following command line:

usage: btyper3 -i </path/to/genome.fasta> -o </path/to/output/directory/> [other options]

Required arguments are:

  -i INPUT, --input INPUT
                        Path to input genome in fasta format
  -o OUTPUT, --output OUTPUT
                        Path to desired output directory

Optional arguments are:

  --ani_species [ANI_SPECIES]
                        Optional argument; True or False; assign genome to a
                        species using FastANI; default = True
  --ani_subspecies [ANI_SUBSPECIES]
                        Optional argument; True or False; assign genome to a
                        subspecies, if relevant, using FastANI; default = True
  --ani_geneflow [ANI_GENEFLOW]
                        Optional argument; True or False; assign genome to a
                        pseudo-gene flow unit using the method described by
                        Carroll, et al. using FastANI; default = False
  --ani_typestrains [ANI_TYPESTRAINS]
                        Optional argument; True or False; calculate ANI values
                        between the query genome relative to all B. cereus
                        s.l. species type strain genomes using FastANI, and
                        report the closest species type strain/highest ANI
                        value; default = False
  --fastani_path [FASTANI_PATH]
                        Optional argument for use with --ani_species True
                        and/or --ani_subspecies True and/or --ani_geneflow
                        True; fastANI, unless path to fastANI executable is
                        supplied; path to fastANI; default = fastANI <fastANI
                        is in the user's path>
  --virulence [VIRULENCE]
                        Optional argument; True or False; perform virulence
                        gene detection (required if one wants to assign
                        genomes to biovars Anthracis or Emeticus); default =
                        True
  --bt [BT]             Optional argument; True or False; perform Bt toxin
                        gene detection for cry, cyt, and vip genes (required
                        if one wants to assign genomes to biovar
                        Thuringiensis); default = True
  --mlst [MLST]         Optional argument; True or False; assign genome to a
                        sequence type (ST) using the seven-gene multi-locus
                        sequence typing (MLST) scheme available in PubMLST;
                        default = True
  --panC [PANC]         Optional argument; True or False; assign genome to a
                        phylogenetic group (Group I-VIII) using an adjusted,
                        eight-group panC group assignment scheme; default =
                        True
  --virulence_db [VIRULENCE_DB]
                        Optional argument for use with --virulence True; aa or
                        nuc; database to use for virulence factor detection:
                        aa for the amino acid sequence database, or nuc for
                        the nucleotide sequence database; option aa uses
                        translated nucleotide blast and allows for the
                        detection of more remote homologs, but is slower than
                        nuc, which uses blastn; default = aa
  --virulence_identity [VIRULENCE_IDENTITY]
                        Optional argument for use with --virulence True;
                        integer from 0 to 100; minimum percent amino
                        acid/nucleotide identity threshold for a virulence
                        gene to be considered present, depending on choice of
                        --virulence_db aa or nuc, respectively; default = 70
  --virulence_coverage [VIRULENCE_COVERAGE]
                        Optional argument for use with --virulence True;
                        integer from 0 to 100; minimum percent coverage
                        threshold for a virulence gene to be considered
                        present; default = 80
  --bt_identity [BT_IDENTITY]
                        Optional argument for use with --bt True; integer from
                        0 to 100; minimum percent amino acid identity
                        threshold for a Bt toxin gene to be considered
                        present; default = 50
  --bt_coverage [BT_COVERAGE]
                        Optional argument for use with --bt True; integer from
                        0 to 100; minimum percent coverage threshold for a Bt
                        toxin gene to be considered present; default = 70
  --bt_overlap [BT_OVERLAP]
                        Optional argument for use with --bt True; float from 0
                        to 1; specify maximum proportion of overlap for
                        overlapping Bt toxin genes to be considered separate
                        genes; Bt toxin genes below this threshold will be
                        considered separate, while those above it will be
                        considered overlapping, and only the top hit will be
                        reported; default=0.7
  --evalue [EVALUE]     Optional argument for use with --virulence True and/or
                        --bt True; float >= 0; maximum blast e-value for a hit
                        to be saved; note that if both --virulence True and
                        --bt True, this e-value threshold will be applied to
                        both analyses; default = 1e-5
  --download_mlst_latest [DOWNLOAD_MLST_LATEST]
                        Optional argument for use with --mlst True; True or
                        False; download the latest version of the seven-gene
                        multi-locus sequence typing (MLST) scheme available in
                        PubMLST; if this is False, BTyper3 will search for the
                        appropriate files in the seq_mlst_db directory;
                        default = False
  --version             Print version

For help:

btyper3 -h

For the version:

btyper3 --version